Homo sapiens |
Synovial Tissues (Hip),Synovial Tissues (Knee) |
Rheumatoid Arthritis |
27282753 |
Joint-specific DNA methylation and transcriptome signatures in rheumatoid arthritis identify distinct pathogenic processes. |
Nature communications |
2016 |
Ai R, Hammaker D, Boyle DL, Morgan R, Walsh AM, Fan S, Firestein GS, Wang W. |
Wei Wang |
Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Dr., La Jolla, California 92093, USA |
PRJNA317757 |
Bulk |
Homo sapiens |
Synovial Tissues |
Arthritis,Healthy Control,Osteoarthritis,Rheumatoid Arthritis,Undifferentiated Arthritis |
28455435 |
CD40L-Dependent Pathway Is Active at Various Stages of Rheumatoid Arthritis Disease Progression. |
Journal of immunology (Baltimore, Md. : 1950) |
2017 |
Guo Y, Walsh AM, Fearon U, Smith MD, Wechalekar MD, Yin X, Cole S, Orr C, McGarry T, Canavan M, Kelly S, Lin TA, Liu X, Proudman SM, Veale DJ, Pitzalis C, Nagpal S. |
Yanxia Guo; Sunil Nagpal |
Immunology, Janssen Research, Spring House, PA 19477, USA |
PRJNA352076 |
Bulk |
Homo sapiens |
Whole blood |
Established Rheumatoid Arthritis,Healthy Control,Newly Diagnosed Rheumatoid Arthritis |
28148290 |
Discovery of new candidate genes for rheumatoid arthritis through integration of genetic association data with expression pathway analysis. |
Arthritis research & therapy |
2017 |
Shchetynsky K, Diaz-Gallo LM, Folkersen L, Hensvold AH, Catrina AI, Berg L, Klareskog L, Padyukov L. |
Klementy Shchetynsky |
Rheumatology Unit, Department of Medicine Centre of Molecular Medicine, CMM:L8:04, Karolinska Institutet/Karolinska University Hospital Solna, 171 61 Stockholm, Sweden |
PRJNA354367 |
Bulk |
Homo sapiens |
Peripheral Blood |
Healthy Control,Rheumatoid Arthritis,Systemic Lupus Erythematosus |
29717110 |
IL-21 drives expansion and plasma cell differentiation of autoreactive CD11chiT-bet+ B cells in SLE. |
Nature communications |
2018 |
Wang S, Wang J, Kumar V, Karnell JL, Naiman B, Gross PS, Rahman S, Zerrouki K, Hanna R, Morehouse C, Holoweckyj N, Liu H, Autoimmunity Molecular Medicine Team, Manna Z, Goldbach-Mansky R, Hasni S, Siegel R, Sanjuan M, Streicher K, Cancro MP, Kolbeck R, Ettinger R. |
Sunil Nagpal |
Immunology, Janssen Research, Spring House, PA 19477, USA |
PRJNA435554 |
Bulk |
Homo sapiens |
Synovial Tissues (Knee) |
Rheumatoid Arthritis |
28863153 |
Triple DMARD treatment in early rheumatoid arthritis modulates synovial T cell activation and plasmablast/plasma cell differentiation pathways. |
PloS one |
2017 |
Walsh AM, Wechalekar MD, Guo Y, Yin X, Weedon H, Proudman SM, Smith MD, Nagpal S. |
Malcolm D. Smith; Sunil Nagpal |
Flinders University, Adelaide, South Australia, Australia; Immunology, Janssen Research, Spring House, PA 19477, USA |
PRJNA380832 |
Bulk |
Homo sapiens |
Whole Blood |
Amyotrophic Lateral Sclerosis,Healthy Control,Multiple Sclerosis,Sepsis,Type 1 Diabetes |
25314013 |
Copy number loss of the interferon gene cluster in melanomas is linked to reduced T cell infiltrate and poor patient prognosis. |
PloS one |
2014 |
Linsley PS, Speake C, Whalen E, Chaussabel D. |
Peter S. Linsley |
Department of Systems Immunology, Benaroya Research Institute, Seattle, WA, United States of America |
PRJNA258216 |
Bulk |
Homo sapiens |
Peripheral Blood |
Healthy Control,Relapsing-Remitting Multiple Sclerosis (Rrms) |
25885816 |
Defective structural RNA processing in relapsing-remitting multiple sclerosis. |
Genome Biology |
2015 |
Spurlock CF, Tossberg JT, Guo Y, Sriram S, Crooke PS, Aune TM. |
Thomas M Aune |
Department of Medicine, Vanderbilt University School of Medicine,Nashville, TN 37232, USA |
PRJNA277352 |
Bulk |
Homo sapiens |
Peripheral Blood |
Healthy Control,Multiple Sclerosis |
25972006 |
Functional inflammatory profiles distinguish myelin-reactive T cells from patients with multiple sclerosis. |
Science translational medicine |
2015 |
Cao Y, Goods BA, Raddassi K, Nepom GT, Kwok WW, Love JC, Hafler DA. |
David A. Hafler |
Department of Neurology and Department of Immunobiology, Yale School of Medicine, New Haven, Connecticut 06520, USA |
PRJNA277876 |
Bulk |
Homo sapiens |
Peripheral Blood |
Healthy Control,Systemic Lupus Erythematosus |
27835693 |
RNA-seq Analysis Reveals Unique Transcriptome Signatures in Systemic Lupus Erythematosus Patients with Distinct Autoantibody Specificities. |
PloS one |
2016 |
Rai R, Chauhan SK, Singh VV, Rai M, Rai G. |
Geeta Rai |
Department of Molecular and Human Genetics, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, India |
PRJNA318253 |
Bulk |
Homo sapiens |
Whole Blood |
Crohn's Disease,Healthy Control,Oligoarticular Juvenile Idiopathic Arthritis,Polyarticular Juvenile Idiopathic Arthritis,Systemic Juvenile Idiopathic Arthritis,Ulcerative Colitis |
29950172 |
Disease-specific regulation of gene expression in a comparative analysis of juvenile idiopathic arthritis and inflammatory bowel disease. |
Genome medicine |
2018 |
Mo A, Marigorta UM, Arafat D, Chan LHK, Ponder L, Jang SR, Prince J, Kugathasan S, Prahalad S, Gibson G. |
Greg Gibson |
Center for Integrative Genomics and School of Biological Sciences, Georgia Institute of Technology, Engineered Biosystems Building, EBB 2115, 950 Atlantic Drive, Atlanta, GA 30332, USA |
PRJNA439192 |
Bulk |
Homo sapiens |
Blood |
Healthy Control,Systemic Sclerosis (SSc) |
29348297 |
Changes in macrophage transcriptome associate with systemic sclerosis and mediate GSDMA contribution to disease risk. |
Annals of the rheumatic diseases |
2018 |
Moreno-Moral A, Bagnati M, Koturan S, Ko JH, Fonseca C, Harmston N, Game L, Martin J, Ong V, Abraham DJ, Denton CP, Behmoaras J, Petretto E. |
Jacques Behmoaras |
Centre for Complement and Inflammation research, Imperial College London, Hammersmith Hospital, London W12 0nn, UK |
PRJNA411909 |
Bulk |
Homo sapiens |
Skin (Antecubital Fossa Left),Skin (Antecubital Fossa Right),Skin (Antecubital Fossa),Skin (Lower Arm Left),Skin (Upper Arm Extensor Left),Skin (Upper Arm Extensor Right),Skin (Upper Arm Flexural Left),Skin (Upper Arm Flexural Right),Skin (Upper Leg Flexural Right),Skin (Upper Upper Arm Flexural Left) |
Atopic Dermatitis,Healthy Control,Psoriasis |
30641038 |
Atopic Dermatitis Is an IL-13-Dominant Disease with Greater Molecular Heterogeneity Compared to Psoriasis. |
The Journal of investigative dermatology |
2019 |
Tsoi LC, Rodriguez E, Degenhardt F, Baurecht H, Wehkamp U, Volks N, Szymczak S, Swindell WR, Sarkar MK, Raja K, Shao S, Patrick M, Gao Y, Uppala R, Perez White BE, Getsios S, Harms PW, Maverakis E, Elder JT, Franke A, Gudjonsson JE, Weidinger S. |
Johann E. Gudjonsson |
Department of Dermatology, University of Michigan, Ann Arbor, Michigan 48109, USA |
PRJNA496323 |
Bulk |
Homo sapiens |
Skin (Arms Or Legs),Skin (Palms Or Soles),Skin (Scalp),Skin (Trunk Or Upper Legs) |
Conventional Plaque Psoriasis,Healthy Control,Palmoplantar Psoriasis,Scalp Psoriasis |
30054515 |
RNA-seq and flow-cytometry of conventional, scalp, and palmoplantar psoriasis reveal shared and distinct molecular pathways. |
Scientific reports |
2018 |
Ahn R, Yan D, Chang HW, Lee K, Bhattarai S, Huang ZM, Nakamura M, Singh R, Afifi L, Taravati K, Munoz-Sandoval P, Pauli M, Rosenblum MD, Liao W. |
Richard Ahn |
Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA |
PRJNA481993 |
Bulk |
Homo sapiens |
Skin |
Chronic Plaque Psoriasis,Healthy Control |
27015450 |
Landscape of Long Noncoding RNAs in Psoriatic and Healthy Skin. |
The Journal of investigative dermatology |
2016 |
Gupta R, Ahn R, Lai K, Mullins E, Debbaneh M, Dimon M, Arron S, Liao W. |
Wilson Liao |
Department of Dermatology, University of California San Francisco, San Francisco, California, USA |
PRJNA301173 |
Bulk |
Homo sapiens |
Skin |
Chronic Plaque Psoriasis,Healthy Control |
27793094 |
Network analysis of psoriasis reveals biological pathways and roles for coding and long non-coding RNAs. |
BMC genomics |
2016 |
Ahn R, Gupta R, Lai K, Chopra N, Arron ST, Liao W. |
Richard Ahn |
Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA |
PRJNA301173 |
Bulk |
Homo sapiens |
Dermis,Epidermis |
Healthy Control,Psoriasis |
29510191 |
Resident T Cells in Resolved Psoriasis Steer Tissue Responses that Stratify Clinical Outcome. |
The Journal of investigative dermatology |
2018 |
Gallais Sérézal I, Classon C, Cheuk S, Barrientos-Somarribas M, Wadman E, Martini E, Chang D, Xu Landén N, Ehrström M, Nylén S, Eidsmo L. |
Liv Eidsmo |
Dermatology and Venerology Unit, Department of Medicine, CMM L8:02, Karolinska Institutet 171 77 Solna, Sweden |
PRJNA401782 |
Bulk |
Homo sapiens |
Skin |
Healthy Control,Psoriasis |
24441097 |
Transcriptome analysis of psoriasis in a large case-control sample: RNA-seq provides insights into disease mechanisms. |
The Journal of investigative dermatology |
2014 |
Li B, Tsoi LC, Swindell WR, Gudjonsson JE, Tejasvi T, Johnston A, Ding J, Stuart PE, Xing X, Kochkodan JJ, Voorhees JJ, Kang HM, Nair RP, Abecasis GR, Elder JT. |
Goncalo R Abecasis; James T Elder |
Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA; Department of Dermatology, University of Michigan, Ann Arbor, MI, USA |
PRJNA236547 |
Bulk |
Homo sapiens |
Skin |
Healthy Control,Psoriasis |
25723451 |
Analysis of long non-coding RNAs highlights tissue-specific expression patterns and epigenetic profiles in normal and psoriatic skin. |
Genome biology |
2015 |
Tsoi LC, Iyer MK, Stuart PE, Swindell WR, Gudjonsson JE, Tejasvi T, Sarkar MK, Li B, Ding J, Voorhees JJ, Kang HM, Nair RP, Chinnaiyan AM, Abecasis GR, Elder JT. |
Goncalo R Abecasis; James T Elder |
Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA; Department of Dermatology, University of Michigan, Ann Arbor, MI, USA |
PRJNA236547 |
Bulk |
Homo sapiens |
Skin |
Healthy Control,Psoriasis |
27992404 |
A gene network regulated by the transcription factor VGLL3 as a promoter of sex-biased autoimmune diseases. |
Nature immunology |
2017 |
Liang Y, Tsoi LC, Xing X, Beamer MA, Swindell WR, Sarkar MK, Berthier CC, Stuart PE, Harms PW, Nair RP, Elder JT, Voorhees JJ, Kahlenberg JM, Gudjonsson JE. |
Johann E. Gudjonsson |
Department of Dermatology, University of Michigan, Ann Arbor Michigan, USA |
PRJNA236547 |
Bulk |
Homo sapiens |
Ileal Pouch,Ileum,Prepouch Ileum |
Familial Adenomatous Polyposis (FAP),Healthy Control,Ulcerative Colitis |
28221248 |
Early Transcriptomic Changes in the Ileal Pouch Provide Insight into the Molecular Pathogenesis of Pouchitis and Ulcerative Colitis. |
Inflammatory bowel diseases |
2017 |
Huang Y, Dalal S, Antonopoulos D, Hubert N, Raffals LH, Dolan K, Weber C, Messer JS, Jabri B, Bendelac A, Eren AM, Rubin DT, Sogin M, Chang EB. |
Eugene B. Chang |
Department of Medicine, Knapp Center for Biomedical Discovery, University of Chicago, Chicago, IL, USA |
PRJNA321131 |
Bulk |
Homo sapiens |
Colon |
Ulcerative Colitis |
26522261 |
Association Between Response to Etrolizumab and Expression of Integrin αE and Granzyme A in Colon Biopsies of Patients With Ulcerative Colitis. |
Gastroenterology |
2016 |
Tew GW, Hackney JA, Gibbons D, Lamb CA, Luca D, Egen JG, Diehl L, Eastham Anderson J, Vermeire S, Mansfield JC, Feagan BG, Panes J, Baumgart DC, Schreiber S, Dotan I, Sandborn WJ, Kirby JA, Irving PM, De Hertogh G, Van Assche GA, Rutgeerts P, O'Byrne S, Hayday A, Keir ME. |
Mary E. Keir |
Genentech Research and Early Development, South San Francisco, California,USA |
PRJNA295143 |
Bulk |
Homo sapiens |
Fibrovascular Membrane,Retina |
Diabetes Mellitus/Proliferative Diabetic Retinopathy,Healthy Control |
28400392 |
Identification of RUNX1 as a Mediator of Aberrant Retinal Angiogenesis. |
Diabetes |
2017 |
Lam JD, Oh DJ, Wong LL, Amarnani D, Park-Windhol C, Sanchez AV, Cardona-Velez J, McGuone D, Stemmer-Rachamimov AO, Eliott D, Bielenberg DR, van Zyl T, Shen L, Gai X, D'Amore PA, Kim LA, Arboleda-Velasquez JF. |
Joseph F. Arboleda-Velasquez; Leo A. Kim; Patricia A. D’Amore |
Department of Ophthalmology, Schepens Eye Research Institute/Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA |
PRJNA363068 |
Bulk |
Homo sapiens |
Dorsolateral Prefrontal Cortex (Brodmann Area 46) |
Bipolar Disorder,Healthy Control |
24393808 |
RNA-sequencing of the brain transcriptome implicates dysregulation of neuroplasticity, circadian rhythms and GTPase binding in bipolar disorder. |
Molecular psychiatry |
2014 |
Akula N, Barb J, Jiang X, Wendland JR, Choi KH, Sen SK, Hou L, Chen DT, Laje G, Johnson K, Lipska BK, Kleinman JE, Corrada-Bravo H, Detera-Wadleigh S, Munson PJ, McMahon FJ. |
FJ McMahon |
Human Genetics Branch, National Institute of Mental Health Intramural Research Program, National Institutes of Health, US Department of Health and Human Services, Bethesda, MD, USA |
PRJNA231202 |
Bulk |
Homo sapiens |
Whole Blood |
Healthy Control,Lyme Disease |
26873097 |
Longitudinal Transcriptome Analysis Reveals a Sustained Differential Gene Expression Signature in Patients Treated for Acute Lyme Disease. |
mBio |
2016 |
Bouquet J, Soloski MJ, Swei A, Cheadle C, Federman S, Billaud JN, Rebman AW, Kabre B, Halpert R, Boorgula M, Aucott JN, Chiu CY. |
Charles Y Chiu |
Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California, USA jaucott@jhmi.edu charles.chiu@ucsf.edu. |
PRJNA266572 |
Bulk |
Homo sapiens |
Bronchus |
Bronchial Dysplasia |
27658890 |
A Randomized Phase IIb Trial of myo-Inositol in Smokers with Bronchial Dysplasia. |
Cancer prevention research (Philadelphia, Pa.) |
2016 |
Lam S, Mandrekar SJ, Gesthalter Y, Allen Ziegler KL, Seisler DK, Midthun DE, Mao JT, Aubry MC, McWilliams A, Sin DD, Shaipanich T, Liu G, Johnson E, Bild A, Lenburg ME, Ionescu DN, Mayo J, Yi JE, Tazelaar H, Harmsen WS, Smith J, Spira AE, Beane J, Limburg PJ, Szabo E, Cancer Prevention Network. |
Eva Szabo |
Division of Cancer Prevention, National Cancer Institute, NIH, Bethesda, Maryland. |
PRJNA341833 |
Bulk |
Homo sapiens |
Lung |
Non-Small Cell Lung Cancer (Adenocarcinoma),Non-Small Cell Lung Cancer (Not Otherwise Specified),Non-Small Cell Lung Cancer (Squamous Cell Carcinoma) |
30325352 |
A radiogenomic dataset of non-small cell lung cancer. |
Scientific data |
2018 |
Bakr S, Gevaert O, Echegaray S, Ayers K, Zhou M, Shafiq M, Zheng H, Benson JA, Zhang W, Leung ANC, Kadoch M, Hoang CD, Shrager J, Quon A, Rubin DL, Plevritis SK, Napel S. |
Sandy Napel |
Department of Radiology, Stanford University School of Medicine, Stanford, CA 94305, USA. |
PRJNA401995 |
Bulk |
Homo sapiens |
Olfactory Bulb |
Esthesioneuroblastomas |
30332658 |
Integrated Multi-omic Analysis of Esthesioneuroblastomas Identifies Two Subgroups Linked to Cell Ontogeny. |
Cell reports |
2018 |
Classe M, Yao H, Mouawad R, Creighton CJ, Burgess A, Allanic F, Wassef M, Leroy X, Verillaud B, Mortuaire G, Bielle F, Le Tourneau C, Kurtz JE, Khayat D, Su X, Malouf GG. |
Gabriel G Malouf |
Department of Medical Oncology, Groupe Hospitalier Pitié-Salpêtrière, Assistance Publique Hôpitaux de Paris, Sorbonnes-Universités, University Pierre and Marie Curie, Paris, France. |
PRJNA487796 |
Bulk |
Homo sapiens |
Whole Blood |
Healthy Control,Rheumatoid Arthritis |
30358109 |
Pharmacodynamic biomarkers and differential effects of TNF- and GM-CSF-targeting biologics in rheumatoid arthritis. |
International journal of rheumatic diseases |
2019 |
Guo X, Wang S, Godwood A, Close D, Ryan PC, Roskos LK, White WI. |
Wendy I White |
Clinical Pharmacology & DMPK, MedImmune, Gaithersburg, Maryland, USA |
PRJNA491863 |
Bulk |
Homo sapiens |
Whole Blood |
Healthy Control,Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) |
30897114 |
Whole blood human transcriptome and virome analysis of ME/CFS patients experiencing post-exertional malaise following cardiopulmonary exercise testing. |
PloS one |
2019 |
Bouquet J, Li T, Gardy JL, Kang X, Stevens S, Stevens J, VanNess M, Snell C, Potts J, Miller RR, Morshed M, McCabe M, Parker S, Uyaguari M, Tang P, Steiner T, Chan WS, De Souza AM, Mattman A, Patrick DM, Chiu CY. |
David M. Patrick; Charles Y. Chiu |
Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, USA |
PRJNA526259 |
Bulk |
Homo sapiens |
Plasma |
Chronic Pancreatitis(CP),Healthy Control,Pancreatic Ductal Adenocarcinoma (PDAC) |
31562239 |
Plasma extracellular vesicle long RNA profiling identifies a diagnostic signature for the detection of pancreatic ductal adenocarcinoma. |
Gut |
2020 |
Yu S, Li Y, Liao Z, Wang Z, Wang Z, Li Y, Qian L, Zhao J, Zong H, Kang B, Zou WB, Chen K, He X, Meng Z, Chen Z, Huang S, Wang P. |
Peng Wang |
Department of Integrative Oncology, Fudan University Shanghai Cancer Center, Shanghai, China |
PRJNA552230 |
Bulk |
Homo sapiens |
Lung |
Healthy Control,SARS-CoV-2 infection |
32416070 |
Imbalanced Host Response to SARS-CoV-2 Drives Development of COVID-19. |
Cell |
2020 |
Blanco-Melo D, Nilsson-Payant BE, Liu WC, Uhl S, Hoagland D, Møller R, Jordan TX, Oishi K, Panis M, Sachs D, Wang TT, Schwartz RE, Lim JK, Albrecht RA, tenOever BR. |
Benjamin R. tenOever |
Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, USA |
PRJNA615032 |
Bulk |
Homo sapiens |
Peripheral Blood |
Healthy Control,Systemic Sclerosis (SSc) |
30804934 |
The Long Non-coding RNA NRIR Drives IFN-Response in Monocytes: Implication for Systemic Sclerosis. |
Frontiers in immunology |
2019 |
Mariotti B, Servaas NH, Rossato M, Tamassia N, Cassatella MA, Cossu M, Beretta L, van der Kroef M, Radstake TRDJ, Bazzoni F. |
Marzia Rossato |
Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht, Utrecht, Netherlands/Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht, Netherlands/Department of Biotechnology, University of Verona, Verona, Italy |
PRJNA510657 |
Bulk |
Homo sapiens |
Blood,Bone Marrow,Pancreas |
Acute B-Lymphoid Leukemia,Chronic Lymphocytic Leukemia (CLL),Myelodysplastic Syndromes(MDS),Pancreatic Cancer |
26565915 |
Cancer-Associated SF3B1 Hotspot Mutations Induce Cryptic 3' Splice Site Selection through Use of a Different Branch Point. |
Cell reports |
2015 |
Darman RB, Seiler M, Agrawal AA, Lim KH, Peng S, Aird D, Bailey SL, Bhavsar EB, Chan B, Colla S, Corson L, Feala J, Fekkes P, Ichikawa K, Keaney GF, Lee L, Kumar P, Kunii K, MacKenzie C, Matijevic M, Mizui Y, Myint K, Park ES, Puyang X, Selvaraj A, Thomas MP, Tsai J, Wang JY, Warmuth M, Yang H, Zhu P, Garcia-Manero G, Furman RR, Yu L, Smith PG, Buonamici S. |
Silvia Buonamici |
H3 Biomedicine, Inc., Cambridge, MA 02139, USA |
PRJNA295064 |
Bulk |
Homo sapiens |
Blood,Bone Marrow,Pancreas |
Acute B-Lymphoid Leukemia,Chronic Lymphocytic Leukemia (CLL),Myelodysplastic Syndromes(MDS),Pancreatic Cancer |
27604819 |
Hemopoietic-specific Sf3b1-K700E knock-in mice display the splicing defect seen in human MDS but develop anemia without ring sideroblasts. |
Leukemia |
2017 |
Mupo A, Seiler M, Sathiaseelan V, Pance A, Yang Y, Agrawal AA, Iorio F, Bautista R, Pacharne S, Tzelepis K, Manes N, Wright P, Papaemmanuil E, Kent DG, Campbell PC, Buonamici S, Bolli N, Vassiliou GS. |
N Bolli; G S Vassiliou |
Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK/Dipartimento di Oncologia ed Onco-Ematologia, Universita’ degli Studi di Milano, Milano, Italy/Dipartimento di Ematologia ed Onco-Ematologia Pediatrica, Fondazione IRCCS Istituto Nazionale dei Tumori, Milano, Italy;Haematological Cancer Genetics, Wellcome Sanger Institute, Hinxton, Cambridge, UK/Department of Haematology, University of Cambridge, Cambridge, UK/Department of Haematology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK |
PRJNA295064 |
Bulk |
Homo sapiens |
Skin |
Cutaneous T-Cell Lymphoma,Healthy Control |
29895574 |
Primary T Cells from Cutaneous T-cell Lymphoma Skin Explants Display an Exhausted Immune Checkpoint Profile. |
Cancer immunology research |
2018 |
Querfeld C, Leung S, Myskowski PL, Curran SA, Goldman DA, Heller G, Wu X, Kil SH, Sharma S, Finn KJ, Horwitz S, Moskowitz A, Mehrara B, Rosen ST, Halpern AC, Young JW. |
Christiane Querfeld |
Laboratory of Cellular Immunobiology, Immunology Program, Sloan Kettering Institute for Cancer Research, Memorial Sloan Kettering Cancer Center/Dermatology Service, Memorial Sloan Kettering Cancer Center/Weill Cornell Medical College, New York, New York, 10065/Beckman Research Institute, City of Hope, Duarte, CA, USA |
PRJNA450035 |
Bulk |
Homo sapiens |
Cornea |
Healthy Control,Keratoconus (KTCN) |
28145428 |
Collagen synthesis disruption and downregulation of core elements of TGF-β, Hippo, and Wnt pathways in keratoconus corneas. |
European journal of human genetics : EJHG |
2017 |
Kabza M, Karolak JA, Rydzanicz M, Szcześniak MW, Nowak DM, Ginter-Matuszewska B, Polakowski P, Ploski R, Szaflik JP, Gajecka M. |
Marzena Gajecka |
Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, Poznan, Poland/Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland |
PRJNA312169 |
Bulk |
Homo sapiens |
Brain |
Autism Spectrum Disorder (ASD),Healthy Control |
26186191 |
FOXG1-Dependent Dysregulation of GABA/Glutamate Neuron Differentiation in Autism Spectrum Disorders. |
Cell |
2015 |
Mariani J, Coppola G, Zhang P, Abyzov A, Provini L, Tomasini L, Amenduni M, Szekely A, Palejev D, Wilson M, Gerstein M, Grigorenko EL, Chawarska K, Pelphrey KA, Howe JR, Vaccarino FM. |
Flora M. Vaccarino |
Program in Neurodevelopment and Regeneration, Yale University, New Haven, CT 06520, USA/Child Study Center, Yale University, New Haven, CT 06520, USA/Department of Neurobiology, Yale University, New Haven, CT 06520, USA |
PRJNA261255 |
Bulk |
Homo sapiens |
Liver,Non-Neoplastic Liver Tissue |
Chronic Hepatitis B virus-associated Hepatocellular carcinoma(HBV-HCC) |
29212479 |
A pilot systematic genomic comparison of recurrence risks of hepatitis B virus-associated hepatocellular carcinoma with low- and high-degree liver fibrosis. |
BMC medicine |
2017 |
Yoo S, Wang W, Wang Q, Fiel MI, Lee E, Hiotis SP, Zhu J. |
Spiros P. Hiotis;Jun Zhu |
Department of Surgery, Division of Surgical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY USA;Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY USA/Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY USA/Sema4, a Mount Sinai venture, Stamford, CT USA |
PRJNA371753 |
Bulk |
Homo sapiens |
Lung |
Healthy Control,Idiopathic Pulmonary Fibrosis |
28230051 |
Cellular senescence mediates fibrotic pulmonary disease. |
Nature communications |
2017 |
Schafer MJ, White TA, Iijima K, Haak AJ, Ligresti G, Atkinson EJ, Oberg AL, Birch J, Salmonowicz H, Zhu Y, Mazula DL, Brooks RW, Fuhrmann-Stroissnigg H, Pirtskhalava T, Prakash YS, Tchkonia T, Robbins PD, Aubry MC, Passos JF, Kirkland JL, Tschumperlin DJ, Kita H, LeBrasseur NK. |
Nathan K. LeBrasseur |
Robert and Arlene Kogod Center on Aging, Mayo Clinic College of Medicine, Mayo Clinic 200 First Street Southwest, Rochester, 55905, Minnesota, USA/Department of Physical Medicine and Rehabilitation, Mayo Clinic College of Medicine, Rochester, 55905, Minnesota, USA/Department of Physiology and Biomedical Engineering, Mayo Clinic College of Medicine, Rochester, 55905, Minnesota, USA |
PRJNA358081 |
Bulk |
Homo sapiens |
Bronchus |
Chronic Obstructive Pulmonary Disease (COPD),Healthy Control |
29472603 |
Bronchial extracellular matrix from COPD patients induces altered gene expression in repopulated primary human bronchial epithelial cells. |
Scientific reports |
2018 |
Hedström U, Hallgren O, Öberg L, DeMicco A, Vaarala O, Westergren-Thorsson G, Zhou X. |
Xiaohong Zhou |
Bioscience Regeneration Department, Respiratory, Inflammation and Autoimmunity, IMED Biotech Unit, AstraZeneca, Gothenburg, Sweden |
PRJNA422059 |
Bulk |
Homo sapiens |
Airway Smooth Muscle |
Asthma,Healthy Control |
30694689 |
Airway Smooth Muscle-Specific Transcriptomic Signatures of Glucocorticoid Exposure. |
American journal of respiratory cell and molecular biology |
2019 |
Kan M, Koziol-White C, Shumyatcher M, Johnson M, Jester W, Panettieri RA, Himes BE. |
Blanca E. Himes |
Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Philadelphia, Pennsylvania, USA |
PRJNA369399 |
Bulk |
Homo sapiens |
Lung |
Lung Adenocarcinoma,Squamous Cell Carcinoma |
29898990 |
MET-Oncogenic and JAK2-Inactivating Alterations Are Independent Factors That Affect Regulation of PD-L1 Expression in Lung Cancer. |
Clinical cancer research : an official journal of the American Association for Cancer Research |
2018 |
Saigi M, Alburquerque-Bejar JJ, Mc Leer-Florin A, Pereira C, Pros E, Romero OA, Baixeras N, Esteve-Codina A, Nadal E, Brambilla E, Sanchez-Cespedes M. |
Montse Sanchez-Cespedes |
Genes and Cancer Group, Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain |
PRJNA431798 |
Bulk |
Homo sapiens |
Peripheral Blood |
Rheumatoid Arthritis,Spondyloarthritis |
30602780 |
RORγt inhibition selectively targets IL-17 producing iNKT and γδ-T cells enriched in Spondyloarthritis patients. |
Nature communications |
2019 |
Venken K, Jacques P, Mortier C, Labadia ME, Decruy T, Coudenys J, Hoyt K, Wayne AL, Hughes R, Turner M, Van Gassen S, Martens L, Smith D, Harcken C, Wahle J, Wang CT, Verheugen E, Schryvers N, Varkas G, Cypers H, Wittoek R, Piette Y, Gyselbrecht L, Van Calenbergh S, Van den Bosch F, Saeys Y, Nabozny G, Elewaut D. |
Koen Venken;Dirk Elewaut |
Department of Rheumatology, Faculty of Medicine and Health Sciences, Laboratory for Molecular Immunology and Inflammation, Ghent University, C. Heymanslaan 10, 9000, Ghent, Belgium/VIB Inflammation Research Center, Ghent University, Technologiepark 71, 9052, Ghent, Belgium;Department of Rheumatology, Faculty of Medicine and Health Sciences, Laboratory for Molecular Immunology and Inflammation, Ghent University, C. Heymanslaan 10, 9000, Ghent, Belgium/VIB Inflammation Research Center, Ghent University, Technologiepark 71, 9052, Ghent, Belgium |
PRJNA505801 |
Bulk |
Homo sapiens |
Lumbar Puncture Cerebrospinal fluid,Ventricular Cerebrospinal fluid |
Non-TB Infection Meningitis or Ventriculitis,Pediatric TB Meningitis |
31434901 |
Tuberculous meningitis in children is characterized by compartmentalized immune responses and neural excitotoxicity. |
Nature communications |
2019 |
Rohlwink UK, Figaji A, Wilkinson KA, Horswell S, Sesay AK, Deffur A, Enslin N, Solomons R, Van Toorn R, Eley B, Levin M, Wilkinson RJ, Lai RPJ. |
Rachel P. J. Lai |
The Francis Crick Institute, London, NW1 1AT UK/Department of Infectious Disease, Imperial College London, London, W2 1PG UK |
PRJNA504827 |
Bulk |
Homo sapiens |
Aortic Endothelium |
Healthy Control,Type 1 Diabetes |
28886276 |
Systems approach to the pharmacological actions of HDAC inhibitors reveals EP300 activities and convergent mechanisms of regulation in diabetes. |
Epigenetics |
2017 |
Rafehi H, Kaspi A, Ziemann M, Okabe J, Karagiannis TC, El-Osta A, El-Osta A. |
Assam El-Osta |
Epigenetics in Human Health and Disease Laboratory, Department of Diabetes, Central Clinical School, Faculty of Medicine, Monash University , Melbourne , Victoria , Australia/Department of Pathology, The University of Melbourne , Parkville , Victoria , Australia/Faculty of Medicine, Nursing and Health Sciences, Department of Diabetes, Monash University , Melbourne , Victoria , Australia/Hong Kong Institute of Diabetes and Obesity, Prince of Wales Hospital, The Chinese University of Hong Kong , Hong Kong SAR |
PRJNA309443 |
Bulk |
Homo sapiens |
Human Trachea-Bronchial Tissues,Trachea Bronchial Tissues |
Asthma,Healthy Control |
25706956 |
Phenotypic responses of differentiated asthmatic human airway epithelial cultures to rhinovirus. |
PloS one |
2015 |
Bai J, Smock SL, Jackson GR, MacIsaac KD, Huang Y, Mankus C, Oldach J, Roberts B, Ma YL, Klappenbach JA, Crackower MA, Alves SE, Hayden PJ. |
Jianwu Bai; Patrick J. Hayden |
Merck Research Laboratories, Boston, Massachusetts, United States of America;MatTek Corporation, Ashland, Massachusetts, United States of America |
PRJNA260343 |
Bulk |
Homo sapiens |
Brain |
Healthy Control,Schizophrenia |
31535015 |
Deconvolution of transcriptional networks identifies TCF4 as a master regulator in schizophrenia. |
Science advances |
2019 |
Doostparast Torshizi A, Armoskus C, Zhang H, Forrest MP, Zhang S, Souaiaia T, Evgrafov OV, Knowles JA, Duan J, Wang K. |
Kai Wang; Jubao Duan |
Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA. Center for Psychiatric Genetics, North Shore University Health System, Evanston, IL 60201, USA |
PRJNA527139 |
Bulk |
Homo sapiens |
Peripheral Blood |
Healthy Control,Type 1 Diabetes |
30910956 |
Risk variants disrupting enhancers of TH1 and TREG cells in type 1 diabetes. |
Proceedings of the National Academy of Sciences of the United States of America |
2019 |
Gao P, Uzun Y, He B, Salamati SE, Coffey JKM, Tsalikian E, Tan K. |
Kai Tan |
Division of Oncology, Children’s Hospital of Philadelphia, Philadelphia, USA |
PRJNA445711 |
Bulk |
Homo sapiens |
Ileum |
Crohn's Disease,Healthy Control |
30589872 |
A distinct epigenetic profile distinguishes stenotic from non-inflamed fibroblasts in the ileal mucosa of Crohn's disease patients. |
PloS one |
2018 |
Li Yim AYF, de Bruyn JR, Duijvis NW, Sharp C, Ferrero E, de Jonge WJ, Wildenberg ME, Mannens MMAM, Buskens CJ, D'Haens GR, Henneman P, Te Velde AA. |
Anje A. te Velde |
Tytgat Institute for Liver and Intestinal Research, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands |
PRJNA389715 |
Bulk |
Homo sapiens |
Prostate Gland |
Prostate Cancer |
30305041 |
Genomic analysis of DNA repair genes and androgen signaling in prostate cancer. |
BMC cancer |
2018 |
Jividen K, Kedzierska KZ, Yang CS, Szlachta K, Ratan A, Paschal BM. |
Bryce M Pascha |
Center for Cell Signaling, University of Virginia, Charlottesville, VA USA |
PRJNA493954 |
Bulk |
Homo sapiens |
Whole Lumbar Spinal Cord |
Familial Amyotrophic Lateral Sclerosis(fALS),Healthy Control,Sporadic Amyotrophic Lateral Sclerosis(sALS) |
25381879 |
Targeting miR-155 restores abnormal microglia and attenuates disease in SOD1 mice. |
Annals of neurology |
2015 |
Butovsky O, Jedrychowski MP, Cialic R, Krasemann S, Murugaiyan G, Fanek Z, Greco DJ, Wu PM, Doykan CE, Kiner O, Lawson RJ, Frosch MP, Pochet N, Fatimy RE, Krichevsky AM, Gygi SP, Lassmann H, Berry J, Cudkowicz ME, Weiner HL. |
Oleg Butovsky; Howard L. Weiner |
Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA |
PRJNA230511 |
Bulk |
Homo sapiens |
Synovial Tissues (Knee) |
Osteoarthritis |
29973527 |
Pain-Associated Transcriptome Changes in Synovium of Knee Osteoarthritis Patients. |
Genes |
2018 |
Bratus-Neuenschwander A, Castro-Giner F, Frank-Bertoncelj M, Aluri S, Fucentese SF, Schlapbach R, Sprott H. |
Anna Bratus-Neuenschwander |
Functional Genomics Center Zurich, University of Zurich/ETH Zurich, 8057 Zurich, Switzerland |
PRJNA389258 |
Bulk |
Homo sapiens |
Brain |
Healthy Control,Obese |
29681516 |
Super-Obese Patient-Derived iPSC Hypothalamic Neurons Exhibit Obesogenic Signatures and Hormone Responses. |
Cell stem cell |
2018 |
Rajamani U, Gross AR, Hjelm BE, Sequeira A, Vawter MP, Tang J, Gangalapudi V, Wang Y, Andres AM, Gottlieb RA, Sareen D. |
Dhruv Sareen |
Board of Governors, Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA |
PRJNA376498 |
Bulk |
Homo sapiens |
Clear Cell Renal Cell Carcinoma Tumor (ccRCC),Kidney |
Clear Cell Renal Cell Carcinoma (ccRCC) |
28893800 |
VHL Deficiency Drives Enhancer Activation of Oncogenes in Clear Cell Renal Cell Carcinoma. |
Cancer discovery |
2017 |
Yao X, Tan J, Lim KJ, Koh J, Ooi WF, Li Z, Huang D, Xing M, Chan YS, Qu JZ, Tay ST, Wijaya G, Lam YN, Hong JH, Lee-Lim AP, Guan P, Ng MSW, He CZ, Lin JS, Nandi T, Qamra A, Xu C, Myint SS, Davies JOJ, Goh JY, Loh G, Tan BC, Rozen SG, Yu Q, Tan IBH, Cheng CWS, Li S, Chang KTE, Tan PH, Silver DL, Lezhava A, Steger G, Hughes JR, Teh BT, Tan P. |
Bin Tean The; Patrick Tan |
Institute of Molecular and Cell Biology, Singapore; Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore. |
PRJNA396588 |
Bulk |
Homo sapiens |
Breast |
Breast Cancer |
28967919 |
Chromosome 1q21.3 amplification is a trackable biomarker and actionable target for breast cancer recurrence. |
Nature medicine |
2017 |
Goh JY, Feng M, Wang W, Oguz G, Yatim SMJM, Lee PL, Bao Y, Lim TH, Wang P, Tam WL, Kodahl AR, Lyng MB, Sarma S, Lin SY, Lezhava A, Yap YS, Lim AST, Hoon DSB, Ditzel HJ, Lee SC, Tan EY, Yu Q. |
Henrik J Ditzel; Soo Chin Lee; Ern Yu Tan; Qiang Yu |
Department of Oncology, Odense University Hospital, Odense, Denmark.Cancer Science Institute of Singapore, National University of Singapore, Singapore.Department of General Surgery, Tan Tock Seng Hospital, Singapore.Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Biopolis, Singapore |
PRJNA327871 |
Bulk |
Homo sapiens |
Liver |
Cirrhosis,Colorectal Cancer,Hepatocellular Carcinoma |
30136421 |
Integrating the Epigenome to Identify Drivers of Hepatocellular Carcinoma. |
Hepatology (Baltimore, Md.) |
2019 |
Hlady RA, Sathyanarayan A, Thompson JJ, Zhou D, Wu Q, Pham K, Lee JH, Liu C, Robertson KD. |
KD Robertson |
Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA |
PRJNA445291 |
Bulk |
Homo sapiens |
Bronchoalveolar Lavage Fluid (BALF) |
Healthy Control,SARS-CoV-2 infection |
32228226 |
Transcriptomic characteristics of bronchoalveolar lavage fluid and peripheral blood mononuclear cells in COVID-19 patients. |
Emerging microbes & infections |
2020 |
Xiong Y, Liu Y, Cao L, Wang D, Guo M, Jiang A, Guo D, Hu W, Yang J, Tang Z, Wu H, Lin Y, Zhang M, Zhang Q, Shi M, Liu Y, Zhou Y, Lan K, Chen Y. |
Yu Zhou; Ke Lan; Yu Chen |
State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, People’s Republic of China |
PRJCA002326 |
Bulk |
Homo sapiens |
Blastocyst,Placenta |
Healthy Control |
29037989 |
Genome wide abnormal DNA methylome of human blastocyst in assisted reproductive technology. |
Journal of genetics and genomics = Yi chuan xue bao |
2017 |
Li G, Yu Y, Fan Y, Li C, Xu X, Duan J, Li R, Kang X, Ma X, Chen X, Ke Y, Yan J, Lian Y, Liu P, Zhao Y, Zhao H, Chen Y, Sun X, Liu J, Qiao J, Liu J. |
Jie Qiao; Jiang Liu |
Ministry of Education Key Laboratory of Assisted Reproduction, and Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Center of Reproductive Medicine, Peking University Third Hospital, Beijing 100191, China.CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, 100101 Beijing, China |
PRJCA000248 |
Bulk |
Homo sapiens |
Early Embryogenesis |
Healthy Control |
29526463 |
Chromatin Accessibility Landscape in Human Early Embryos and Its Association with Evolution. |
Cell |
2018 |
Gao L, Wu K, Liu Z, Yao X, Yuan S, Tao W, Yi L, Yu G, Hou Z, Fan D, Tian Y, Liu J, Chen ZJ, Liu J. |
Jianqiao Liu; Zi-Jiang Chen; Jiang Liu |
Center for Reproductive Medicine, Third Affiliated Hospital, Guangzhou Medical University, Guangzhou, China; Center for Reproductive Medicine, Shandong University, National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Key Laboratory of Reproductive Endocrinology, Shandong University, Ministry of Education, Jinan, 250001 Shandong, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China |
PRJCA000484 |
Bulk |
Homo sapiens |
- |
Healthy Control,Zika Virus |
30333476 |
Zika virus shedding in the stool and infection through the anorectal mucosa in mice. |
Emerging microbes & infections |
2018 |
Li C, Deng YQ, Zu S, Quanquin N, Shang J, Tian M, Ji X, Zhang NN, Dong HL, Xu YP, Zhao LZ, Zhang FC, Li XF, Wu A, Cheng G, Qin CF. |
Genhong Cheng; Cheng-Feng Qin |
Center for Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China; Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071 China |
PRJCA000776 |
Bulk |
Homo sapiens |
- |
Healthy Control,Zika Virus |
31527024 |
Azithromycin Protects against Zika virus Infection by Upregulating virus-induced Type I and III Interferon Responses. |
Antimicrobial agents and chemotherapy |
2019 |
Li C, Zu S, Deng YQ, Li D, Parvatiyar K, Quanquin N, Shang J, Sun N, Su J, Liu Z, Wang M, Aliyari SR, Li XF, Wu A, Ma F, Shi Y, Nielsevn-Saines K, Jung JU, Qin FX, Qin CF, Cheng G. |
Genhong Cheng; Cheng-Feng Qin |
Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, California, USA; Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China |
PRJCA000776 |
Bulk |
Homo sapiens |
Whole Blood |
Ischemic Stroke |
31178893 |
A Systems Analysis of the Relationships Between Anemia and Ischemic Stroke Rehabilitation Based on RNA-Seq Data. |
Frontiers in genetics |
2019 |
Wang Y, Huang X, Liu J, Zhao X, Yu H, Cai Y. |
Yunpeng Cai; Haibo Yu |
Research Center for Biomedical Information Technology, Shenzhen Institutes of Advanced Technologies, Chinese Academy of Sciences, Shenzhen, China; Shenzhen Traditional Chinese Medicine Hospital, Shenzhen, China |
PRJCA001265 |
Bulk |
Homo sapiens |
- |
Healthy Control,Recessive Dystrophic Epidermolysis Bullosa (RDEB) |
29630593 |
A multitask clustering approach for single-cell RNA-seq analysis in Recessive Dystrophic Epidermolysis Bullosa. |
PLoS computational biology |
2018 |
Zhang H, Lee CAA, Li Z, Garbe JR, Eide CR, Petegrosso R, Kuang R, Tolar J. |
Tolar Jakub |
Department of Computer Science and Engineering, University of Minnesota Twin Cities, Minneapolis, Minnesota, USA. |
PRJNA428940 |
scRNA |
Homo sapiens |
- |
Healthy Control |
29427839 |
Single-cell RNA sequencing reveals metallothionein heterogeneity during hESC differentiation to definitive endoderm. |
Stem cell research |
2018 |
Lu J, Baccei A, Lummertz da Rocha E, Guillermier C, McManus S, Finney LA, Zhang C, Steinhauser ML, Li H, Lerou PH. |
Paul H Lerou |
Department of Pediatrics, Division of Neonatology and Newborn Medicine, Massachusetts General Hospital for Children, Harvard Medical School, Boston, MA 02114, USA. |
PRJNA432506 |
scRNA |
Homo sapiens |
- |
Healthy Control |
29486586 |
Single-Cell Transcriptomics of Human Oocytes: Environment-Driven Metabolic Competition and Compensatory Mechanisms During Oocyte Maturation. |
Antioxidants & redox signaling |
2019 |
Zhao H, Li T, Zhao Y, Tan T, Liu C, Liu Y, Chang L, Huang N, Li C, Fan Y, Yu Y, Li R, Qiao J. |
Qiao Jie |
Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology and Key Laboratory of Assisted Reproduction, Ministry of Education, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital , Beijing, China |
PRJNA434577 |
scRNA |
Homo sapiens |
- |
Healthy Control |
30681766 |
CRX Expression in Pluripotent Stem Cell-Derived Photoreceptors Marks a Transplantable Subpopulation of Early Cones. |
Stem cells (Dayton, Ohio) |
2019 |
Collin J, Zerti D, Queen R, Santos-Ferreira T, Bauer R, Coxhead J, Hussain R, Steel D, Mellough C, Ader M, Sernagor E, Armstrong L, Lako M. |
Majlinda Lako |
Institute of Genetic Medicine, Newcastle University, Newcastle, United Kingdom. |
PRJNA448011 |
scRNA |
Homo sapiens |
- |
Healthy Control |
30463007 |
The Molecular Signature of Megakaryocyte-Erythroid Progenitors Reveals a Role for the Cell Cycle in Fate Specification. |
Cell reports |
2018 |
Lu YC, Sanada C, Xavier-Ferrucio J, Wang L, Zhang PX, Grimes HL, Venkatasubramanian M, Chetal K, Aronow B, Salomonis N, Krause DS. |
Diane S Krause |
Department of Laboratory Medicine and Yale Stem Cell Center, Yale School of Medicine, 333 Cedar Street, New Haven, CT 06510, USA. Electronic address: yi-chien.lu@yale.edu. |
PRJNA448755 |
scRNA |
Homo sapiens |
Lung Adenocarcinoma,Lung Juxtatumor |
Lung Adenocarcinoma |
30926812 |
Wnt1 silences chemokine genes in dendritic cells and induces adaptive immune resistance in lung adenocarcinoma. |
Nature communications |
2019 |
Kerdidani D, Chouvardas P, Arjo AR, Giopanou I, Ntaliarda G, Guo YA, Tsikitis M, Kazamias G, Potaris K, Stathopoulos GT, Zakynthinos S, Kalomenidis I, Soumelis V, Kollias G, Tsoumakidou M. |
Maria Tsoumakidou |
Division of Immunology, Biomedical Sciences Research Center Alexander Fleming, Vari-Athens, 16672, Greece |
PRJNA510981 |
scRNA |
Homo sapiens |
- |
Healthy Control |
28111004 |
Single cell sequencing reveals heterogeneity within ovarian cancer epithelium and cancer associated stromal cells. |
Gynecologic oncology |
2017 |
Winterhoff BJ, Maile M, Mitra AK, Sebe A, Bazzaro M, Geller MA, Abrahante JE, Klein M, Hellweg R, Mullany SA, Beckman K, Daniel J, Starr TK. |
Timothy K Starr |
Department of Obstetrics, Gynecology & Women's Health, University of Minnesota, Minneapolis, MN, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA. |
PRJNA508840 |
scRNA |
Homo sapiens |
Cord Blood |
Healthy Control |
24925914 |
Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma. |
Science (New York, N.Y.) |
2014 |
Patel AP, Tirosh I, Trombetta JJ, Shalek AK, Gillespie SM, Wakimoto H, Cahill DP, Nahed BV, Curry WT, Martuza RL, Louis DN, Rozenblatt-Rosen O, Suvà ML, Regev A, Bernstein BE. |
Bradley E Bernstein |
Department of Neurosurgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA. Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA. Broad Institute of Harvard and Massachusetts Institute of Techonology (MIT), Cambridge, MA 02142, USA. Howard Hughes Medical Institute Chevy Chase, MD 20815, USA. |
PRJNA392305 |
scRNA |
Homo sapiens |
Bone Marrow |
Chronic Myelogenous Leukemia |
31068472 |
Prosurvival kinase PIM2 is a therapeutic target for eradication of chronic myeloid leukemia stem cells. |
Proceedings of the National Academy of Sciences of the United States of America |
2019 |
Ma L, Pak ML, Ou J, Yu J, St Louis P, Shan Y, Hutchinson L, Li S, Brehm MA, Zhu LJ, Green MR. |
Lihua Julie Zhu |
Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA |
PRJNA322448 |
scRNA |
Homo sapiens |
- |
Prostate Cancer |
29233929 |
Single-Cell RNA-seq Reveals a Subpopulation of Prostate Cancer Cells with Enhanced Cell-Cycle-Related Transcription and Attenuated Androgen Response. |
Cancer research |
2018 |
Horning AM, Wang Y, Lin CK, Louie AD, Jadhav RR, Hung CN, Wang CM, Lin CL, Kirma NB, Liss MA, Kumar AP, Sun L, Liu Z, Chao WT, Wang Q, Jin VX, Chen CL, Huang TH. |
Tim H-M Huang |
Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA |
PRJNA389624 |
scRNA |
Homo sapiens |
- |
Tumorigenesis |
30819896 |
COX-2 mediates tumor-stromal prolactin signaling to initiate tumorigenesis. |
Proceedings of the National Academy of Sciences of the United States of America |
2019 |
Zheng Y, Comaills V, Burr R, Boulay G, Miyamoto DT, Wittner BS, Emmons E, Sil S, Koulopoulos MW, Broderick KT, Tai E, Rengarajan S, Kulkarni AS, Shioda T, Wu CL, Ramaswamy S, Ting DT, Toner M, Rivera MN, Maheswaran S, Haber DA. |
Daniel A Haber |
Massachusetts General Hospital Cancer Center,Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA |
PRJNA521167 |
Bulk;scRNA |
Homo sapiens |
- |
Non-Typhoidal Salmonella (NTS) |
30451854 |
Invasive Salmonella exploits divergent immune evasion strategies in infected and bystander dendritic cell subsets. |
Nature communications |
2018 |
Aulicino A, Rue-Albrecht KC, Preciado-Llanes L, Napolitani G, Ashley N, Cribbs A, Koth J, Lagerholm BC, Ambrose T, Gordon MA, Sims D, Simmons A, Simmons A. |
Alison Simmons |
MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK. |
PRJNA437328 |
scRNA |
Homo sapiens |
- |
Human Immunodeficiency Virus Infection |
29694901 |
Single-Cell RNA-Seq Reveals Transcriptional Heterogeneity in Latent and Reactivated HIV-Infected Cells. |
Cell reports |
2018 |
Golumbeanu M, Cristinelli S, Rato S, Munoz M, Cavassini M, Beerenwinkel N, Ciuffi A. |
Angela Ciuffi |
Department of Biosystems Science and Engineering, ETH Zurich, Basel 4058, Switzerland; SIB Swiss Institute of Bioinformatics, Basel 4058, Switzerland. |
PRJNA437966 |
scRNA |
Homo sapiens |
Breast Epithelium |
Breast Cancer |
31428694 |
Single-cell landscape in mammary epithelium reveals bipotent-like cells associated with breast cancer risk and outcome. |
Communications biology |
2019 |
Chen W, Morabito SJ, Kessenbrock K, Enver T, Meyer KB, Teschendorff AE. |
Andrew E Teschendorff |
CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031 China. |
PRJNA450372 |
scRNA |
Homo sapiens |
Esophagus,Large Intestine,Small Intestine,Stomach |
Healthy Control |
29802404 |
Tracing the temporal-spatial transcriptome landscapes of the human fetal digestive tract using single-cell RNA-sequencing. |
Nature cell biology |
2018 |
Gao S, Yan L, Wang R, Li J, Yong J, Zhou X, Wei Y, Wu X, Wang X, Fan X, Yan J, Zhi X, Gao Y, Guo H, Jin X, Wang W, Mao Y, Wang F, Wen L, Fu W, Ge H, Qiao J, Tang F. |
Fuchou Tang |
Department of Obstetrics and Gynecology, Beijing Advanced Innovation Center for Genomics, College of Life Sciences, Third Hospital, Peking University, Beijing, China |
PRJNA377736 |
scRNA |
Homo sapiens |
Bone Marrow |
Age-Dependent Functional Decline |
30275468 |
Cell-specific proteome analyses of human bone marrow reveal molecular features of age-dependent functional decline. |
Nature communications |
2018 |
Hennrich ML, Romanov N, Horn P, Jaeger S, Eckstein V, Steeples V, Ye F, Ding X, Poisa-Beiro L, Lai MC, Lang B, Boultwood J, Luft T, Zaugg JB, Pellagatti A, Bork P, Aloy P, Gavin AC, Ho AD. |
Anthony D Ho |
European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstrasse 1, Heidelberg, D69117, Germany |
PRJNA473344 |
scRNA |
Homo sapiens |
Bone Marrow |
Multiple Myeloma |
30607001 |
Molecular signatures of multiple myeloma progression through single cell RNA-Seq. |
Blood cancer journal |
2019 |
Jang JS, Li Y, Mitra AK, Bi L, Abyzov A, van Wijnen AJ, Baughn LB, Van Ness B, Rajkumar V, Kumar S, Jen J. |
Jin Jen |
Genome Analysis Core, Medical Genome Facility, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA |
PRJNA487220 |
scRNA |
Homo sapiens |
- |
Pancreatic Cancer |
31155233 |
Stromal Microenvironment Shapes the Intratumoral Architecture of Pancreatic Cancer. |
Cell |
2019 |
Ligorio M, Sil S, Malagon-Lopez J, Nieman LT, Misale S, Di Pilato M, Ebright RY, Karabacak MN, Kulkarni AS, Liu A, Vincent Jordan N, Franses JW, Philipp J, Kreuzer J, Desai N, Arora KS, Rajurkar M, Horwitz E, Neyaz A, Tai E, Magnus NKC, Vo KD, Yashaswini CN, Marangoni F, Boukhali M, Fatherree JP, Damon LJ, Xega K, Desai R, Choz M, Bersani F, Langenbucher A, Thapar V, Morris R, Wellner UF, Schilling O, Lawrence MS, Liss AS, Rivera MN, Deshpande V, Benes CH, Maheswaran S, Haber DA, Fernandez-Del-Castillo C, Ferrone CR, Haas W, Aryee MJ, Ting DT. |
David T Ting |
Cancer Center, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Surgery, Massachusetts General Hospital, Boston, MA 02114, USA |
PRJNA464359 |
scRNA |
Homo sapiens |
- |
Glioblastoma,Healthy Control |
31151460 |
Single-cell RNA sequencing reveals the impact of chromosomal instability on glioblastoma cancer stem cells. |
BMC medical genomics |
2019 |
Zhao Y, Carter R, Natarajan S, Varn FS, Compton DA, Gawad C, Cheng C, Godek KM. |
Kristina M Godek |
Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA |
PRJNA546254 |
scRNA |
Homo sapiens |
Preimplantation Embryos |
Healthy Control |
23934149 |
Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells. |
Nature structural & molecular biology |
2013 |
Yan L, Yang M, Guo H, Yang L, Wu J, Li R, Liu P, Lian Y, Zheng X, Yan J, Huang J, Li M, Wu X, Wen L, Lao K, Li R, Qiao J, Tang F. |
Ruiqiang Li; Jie Qiao; Fuchou Tang |
Biodynamic Optical Imaging Center and Center for Reproductive Medicine, College of Life Sciences, Third Hospital, Peking University, Beijing, China |
PRJNA153427 |
scRNA |
Homo sapiens |
- |
Healthy control |
24658644 |
The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells. |
Nature biotechnology |
2014 |
Trapnell C, Cacchiarelli D, Grimsby J, Pokharel P, Li S, Morse M, Lennon NJ, Livak KJ, Mikkelsen TS, Rinn JL. |
John L. Rinn |
Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA |
PRJNA229164 |
Bulk;scRNA |
Homo sapiens |
Embryo |
Healthy Control |
26904963 |
Human oocyte developmental potential is predicted by mechanical properties within hours after fertilization. |
Nature communications |
2016 |
Yanez LZ, Han J, Behr BB, Pera RAR, Camarillo DB. |
David B. Camarillo; Livia Z. Yanez |
Department of Bioengineering, Stanford University School of Engineering, Stanford, California 94305, USA |
PRJNA274140 |
scRNA |
Homo sapiens |
Embryo |
Healthy Control |
26293300 |
Defining the three cell lineages of the human blastocyst by single-cell RNA-seq. |
Development (Cambridge, England) |
2015 |
Blakeley P, Fogarty NM, del Valle I, Wamaitha SE, Hu TX, Elder K, Snell P, Christie L, Robson P, Niakan KK. |
Kathy K. Niakan |
Human Embryology and Stem Cell Laboratory, The Francis Crick Institute, Mill Hill Laboratory, London NW7 1AA, UK |
PRJNA277181 |
scRNA |
Homo sapiens |
Cortex,Hippocampus |
Healthy Control |
26060301 |
A survey of human brain transcriptome diversity at the single cell level. |
Proceedings of the National Academy of Sciences of the United States of America |
2015 |
Darmanis S, Sloan SA, Zhang Y, Enge M, Caneda C, Shuer LM, Hayden Gephart MG, Barres BA, Quake SR. |
Ben A. Barresc; Stephen R. Quakea |
Departments of Neurobiology, Stanford University, Stanford, CA, 94305.Departments of Bioengineering, Stanford University, Stanford, CA 94305, USA |
PRJNA281204 |
scRNA |
Homo sapiens |
Lung |
Lung Cancer |
26084335 |
Single-cell mRNA sequencing identifies subclonal heterogeneity in anti-cancer drug responses of lung adenocarcinoma cells. |
Genome biology |
2015 |
Kim KT, Lee HW, Lee HO, Kim SC, Seo YJ, Chung W, Eum HH, Nam DH, Kim J, Joo KM, Park WY. |
Kyeung Min Joo; Woong-Yang Park |
Departments of Anatomy and Cell Biology, Sungkyunkwan University; School of Medicine, Seoul, South Korea.Samsung Genome Institute, Samsung Medical Center, Seoul, South Korea |
PRJNA285793 |
scRNA |
Homo sapiens |
- |
Healthy Control |
26740550 |
Assessing similarity to primary tissue and cortical layer identity in induced pluripotent stem cell-derived cortical neurons through single-cell transcriptomics. |
Human molecular genetics |
2016 |
Handel AE, Chintawar S, Lalic T, Whiteley E, Vowles J, Giustacchini A, Argoud K, Sopp P, Nakanishi M, Bowden R, Cowley S, Newey S, Akerman C, Ponting CP, Cader MZ. |
M. Zameel Cader |
Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, Oxfordshire OX3 9DS, UK |
PRJNA286775 |
scRNA |
Homo sapiens |
- |
Healthy Control |
26524239 |
Fixed single-cell transcriptomic characterization of human radial glial diversity. |
Nature methods |
2016 |
Thomsen ER, Mich JK, Yao Z, Hodge RD, Doyle AM, Jang S, Shehata SI, Nelson AM, Shapovalova NV, Levi BP, Ramanathan S. |
Boaz P. Levi; Sharad Ramanathan |
Allen Institute for Brain Science, Seattle, WA., USA |
PRJNA292324 |
scRNA |
Homo sapiens |
- |
Metastatic Renal Cell Carcinoma,Primary Renal Cell Carcinoma |
27139883 |
Application of single-cell RNA sequencing in optimizing a combinatorial therapeutic strategy in metastatic renal cell carcinoma. |
Genome biology |
2016 |
Kim KT, Lee HW, Lee HO, Song HJ, Jeong da E, Shin S, Kim H, Shin Y, Nam DH, Jeong BC, Kirsch DG, Joo KM, Park WY. |
Kyeung Min Joo; Woong-Yang Park |
Departments of Anatomy and Cell Biology, Sungkyunkwan University; School of Medicine, Seoul, South Korea.Samsung Genome Institute, Samsung Medical Center, Seoul, South Korea |
PRJNA296119 |
scRNA |
Homo sapiens |
Cerebral Organoid |
Healthy Control |
27263970 |
A Primate lncRNA Mediates Notch Signaling during Neuronal Development by Sequestering miRNA. |
Neuron |
2016 |
Rani N, Nowakowski TJ, Zhou H, Godshalk SE, Lisi V, Kriegstein AR, Kosik KS. |
Kenneth S. Kosik |
Neuroscience Research Institute and Department Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA |
PRJNA299330 |
scRNA |
Homo sapiens |
Breast |
Breast Cancer,Metastatic Breast Cancer,Primary Breast Cancer |
28474673 |
Single-cell RNA-seq enables comprehensive tumour and immune cell profiling in primary breast cancer. |
Nature communications |
2017 |
Chung W, Eum HH, Lee HO, Lee KM, Lee HB, Kim KT, Ryu HS, Kim S, Lee JE, Park YH, Kan Z, Han W, Park WY. |
Wonshik Han; Woong-Yang Park |
Department of Surgery and Cancer Research Institute, Seoul National University College of Medicine, Seoul 03080, Korea.Samsung Genome Institute, Samsung Medical Center, Seoul 06351, Korea. |
PRJNA305054 |
scRNA |
Homo sapiens |
- |
Healthy Control |
28045081 |
Batch effects and the effective design of single-cell gene expression studies. |
Scientific reports |
2017 |
Tung PY, Blischak JD, Hsiao CJ, Knowles DA, Burnett JE, Pritchard JK, Gilad Y. |
Yoav Gilad |
Department of Human Genetics, University of Chicago, Chicago, Illinois, USA |
PRJNA309972 |
scRNA |
Homo sapiens |
- |
Myeloproliferative Disease |
28346451 |
SC3: consensus clustering of single-cell RNA-seq data. |
Nature methods |
2017 |
Kiselev VY, Kirschner K, Schaub MT, Andrews T, Yiu A, Chandra T, Natarajan KN, Reik W, Barahona M, Green AR, Hemberg M. |
Martin Hemberg |
Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK |
PRJNA314949 |
scRNA |
Homo sapiens |
Skin |
Melanoma |
29614062 |
Pseudotime Dynamics in Melanoma Single-Cell Transcriptomes Reveals Different Mechanisms of Tumor Progression. |
Biology |
2018 |
Loeffler-Wirth H, Binder H, Willscher E, Gerber T, Kunz M. |
Manfred Kunz |
Department of Dermatology, Venereology and Allergology, University of Leipzig, 04103 Leipzig, Germany |
PRJNA321420 |
scRNA |
Homo sapiens |
- |
Healthy Control |
27568284 |
Zika Virus Disrupts Phospho-TBK1 Localization and Mitosis in Human Neuroepithelial Stem Cells and Radial Glia. |
Cell reports |
2016 |
Onorati M, Li Z, Liu F, Sousa AMM, Nakagawa N, Li M, Dell'Anno MT, Gulden FO, Pochareddy S, Tebbenkamp ATN, Han W, Pletikos M, Gao T, Zhu Y, Bichsel C, Varela L, Szigeti-Buck K, Lisgo S, Zhang Y, Testen A, Gao XB, Mlakar J, Popovic M, Flamand M, Strittmatter SM, Kaczmarek LK, Anton ES, Horvath TL, Lindenbach BD, Sestan N. |
Tamas L. Horvath; Brett D. Lindenbach; Nenad Sestan |
Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA.Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT 06510, USA.Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA. |
PRJNA321741 |
scRNA |
Homo sapiens |
- |
Healthy Control |
27926872 |
Deletion of the Polycomb-Group Protein EZH2 Leads to Compromised Self-Renewal and Differentiation Defects in Human Embryonic Stem Cells. |
Cell reports |
2016 |
Collinson A, Collier AJ, Morgan NP, Sienerth AR, Chandra T, Andrews S, Rugg-Gunn PJ. |
Peter J. Rugg-Gunn |
Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, UK |
PRJNA322291 |
scRNA |
Homo sapiens |
Pancreatic Islet |
Healthy Control |
28965763 |
Single-Cell Analysis of Human Pancreas Reveals Transcriptional Signatures of Aging and Somatic Mutation Patterns. |
Cell |
2017 |
Enge M, Arda HE, Mignardi M, Beausang J, Bottino R, Kim SK, Quake SR. |
Stephen R. Quake |
Department of Bioengineering and Applied Physics, Stanford University, Stanford, CA 94305, USA |
PRJNA322355 |
scRNA |
Homo sapiens |
- |
Diffuse Intrinsic Pontine Glioma (DIPG) |
31534222 |
Electrical and synaptic integration of glioma into neural circuits. |
Nature |
2019 |
Venkatesh HS, Morishita W, Geraghty AC, Silverbush D, Gillespie SM, Arzt M, Tam LT, Espenel C, Ponnuswami A, Ni L, Woo PJ, Taylor KR, Agarwal A, Regev A, Brang D, Vogel H, Hervey-Jumper S, Bergles DE, Suvà ML, Malenka RC, Monje M. |
Michelle Monje |
Department of Neurology, Stanford University, Stanford, CA 94305, USA |
PRJNA554601 |
scRNA |
Homo sapiens |
- |
Healthy Control |
28930664 |
Aryl Hydrocarbon Receptor Controls Monocyte Differentiation into Dendritic Cells versus Macrophages. |
Immunity |
2017 |
Goudot C, Coillard A, Villani AC, Gueguen P, Cros A, Sarkizova S, Tang-Huau TL, Bohec M, Baulande S, Hacohen N, Amigorena S, Segura E. |
Elodie Segura |
Institut Curie, PSL Research University, INSERM, U932, 26 rue d’Ulm, 75005 Paris, France |
PRJNA401805 |
scRNA |
Homo sapiens |
- |
Healthy Control |
29352091 |
Precursors of human CD4+ cytotoxic T lymphocytes identified by single-cell transcriptome analysis. |
Science immunology |
2018 |
Patil VS, Madrigal A, Schmiedel BJ, Clarke J, O'Rourke P, de Silva AD, Harris E, Peters B, Seumois G, Weiskopf D, Sette A, Vijayanand P. |
Pandurangan Vijayanand |
Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA |
PRJNA417193 |
scRNA |
Homo sapiens |
- |
Breast Cancer |
30089904 |
Genetic and transcriptional evolution alters cancer cell line drug response. |
Nature |
2018 |
Ben-David U, Siranosian B, Ha G, Tang H, Oren Y, Hinohara K, Strathdee CA, Dempster J, Lyons NJ, Burns R, Nag A, Kugener G, Cimini B, Tsvetkov P, Maruvka YE, O'Rourke R, Garrity A, Tubelli AA, Bandopadhayay P, Tsherniak A, Vazquez F, Wong B, Birger C, Ghandi M, Thorner AR, Bittker JA, Meyerson M, Getz G, Beroukhim R, Golub TR. |
Rameen Beroukhim; Todd R. Golub |
Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA |
PRJNA471582 |
scRNA |
Homo sapiens |
Embryonic Kidney |
Healthy Control |
30789893 |
Single-cell transcriptomics reveals gene expression dynamics of human fetal kidney development. |
PLoS biology |
2019 |
Hochane M, van den Berg PR, Fan X, Bérenger-Currias N, Adegeest E, Bialecka M, Nieveen M, Menschaart M, Chuva de Sousa Lopes SM, Semrau S. |
Susana M. Chuva de Sousa Lopes; Stefan SemrauI |
Department of Anatomy and Embryology, Leiden University Medical Center, Leiden, The Netherlands.Leiden Institute of Physics, Leiden University, Leiden, The Netherlands |
PRJNA471694 |
scRNA |
Homo sapiens |
Blood |
Healthy Control |
30575716 |
Molecular and functional heterogeneity of IL-10-producing CD4+ T cells. |
Nature communications |
2018 |
Brockmann L, Soukou S, Steglich B, Czarnewski P, Zhao L, Wende S, Bedke T, Ergen C, Manthey C, Agalioti T, Geffken M, Seiz O, Parigi SM, Sorini C, Geginat J, Fujio K, Jacobs T, Roesch T, Izbicki JR, Lohse AW, Flavell RA, Krebs C, Gustafsson JA, Antonson P, Roncarolo MG, Villablanca EJ, Gagliani N, Huber S. |
Nicola Gagliani; Samuel Huber |
Department of Medicine, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany. |
PRJNA496578 |
scRNA |
Homo sapiens |
Testis |
Healthy Control |
30726734 |
The Neonatal and Adult Human Testis Defined at the Single-Cell Level. |
Cell reports |
2019 |
Sohni A, Tan K, Song HW, Burow D, de Rooij DG, Laurent L, Hsieh TC, Rabah R, Hammoud SS, Vicini E, Wilkinson MF. |
Miles F. Wilkinson |
Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA 92093, USA |
PRJNA511433 |
scRNA |
Homo sapiens |
- |
Healthy Control |
31118283 |
Single-cell RNA sequencing unveils the shared and the distinct cytotoxic hallmarks of human TCRVδ1 and TCRVδ2 γδ T lymphocytes. |
Proceedings of the National Academy of Sciences of the United States of America |
2019 |
Pizzolato G, Kaminski H, Tosolini M, Franchini DM, Pont F, Martins F, Valle C, Labourdette D, Cadot S, Quillet-Mary A, Poupot M, Laurent C, Ysebaert L, Meraviglia S, Dieli F, Merville P, Milpied P, Déchanet-Merville J, Fournié JJ. |
Jean-Jacques Fournié |
Centre de Recherches en Cancérologie de Toulouse, INSERM UMR1037, 31100 Toulouse, France |
PRJNA526841 |
scRNA |
Homo sapiens |
Ascites,Bone Marrow,Bone Marrow And Pleural Effusion,Primary Refractory Bone Marrow,Primary Refractory Bone Marrow And Ascites |
Multiple Myeloma |
31558476 |
Alterations in the Transcriptional Programs of Myeloma Cells and the Microenvironment during Extramedullary Progression Affect Proliferation and Immune Evasion. |
Clinical cancer research : an official journal of the American Association for Cancer Research |
2020 |
Ryu D, Kim SJ, Hong Y, Jo A, Kim N, Kim HJ, Lee HO, Kim K, Park WY. |
Hae-Ock Lee; Kihyun Kim; Woong-Yang Park |
Samsung Genome Institute, Samsung Medical Center, Seoul, Korea; Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.Samsung Genome Institute, Samsung Medical Center, Seoul, Korea |
PRJNA415945 |
Bulk;scRNA |
Homo sapiens |
Lung |
Dyskeratosis Congenita,Healthy Control,Idiopathic Pulmonary Fibrosis,Scleroderma |
28737769 |
Local lung hypoxia determines epithelial fate decisions during alveolar regeneration. |
Nature cell biology |
2017 |
Xi Y, Kim T, Brumwell AN, Driver IH, Wei Y, Tan V, Jackson JR, Xu J, Lee DK, Gotts JE, Matthay MA, Shannon JM, Chapman HA, Vaughan AE. |
Harold A. Chapman |
Department of Medicine, Cardiovascular Research Institute, UCSF, San Francisco, California, 94143 USA |
PRJNA326167 |
scRNA |
Homo sapiens |
Melanoma |
Melanoma |
30804224 |
BRN2 suppresses apoptosis, reprograms DNA damage repair, and is associated with a high somatic mutation burden in melanoma. |
Genes & development |
2019 |
Herbert K, Binet R, Lambert JP, Louphrasitthiphol P, Kalkavan H, Sesma-Sanz L, Robles-Espinoza CD, Sarkar S, Suer E, Andrews S, Chauhan J, Roberts ND, Middleton MR, Gingras AC, Masson JY, Larue L, Falletta P, Goding CR. |
Colin R Goding; Lionel Larue; Paola Falletta |
Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, UK. |
PRJNA513348 |
Bulk |
Homo sapiens |
Brain |
Healthy Control |
29915193 |
Direct pericyte-to-neuron reprogramming via unfolding of a neural stem cell-like program. |
Nature neuroscience |
2018 |
Karow M, Camp JG, Falk S, Gerber T, Pataskar A, Gac-Santel M, Kageyama J, Brazovskaja A, Garding A, Fan W, Riedemann T, Casamassa A, Smiyakin A, Schichor C, Götz M, Tiwari VK, Treutlein B, Berninger B. |
|
|
PRJNA464430 |
scRNA |
Homo sapiens |
Prefrontal Cortex |
Healthy Control |
29539641 |
A single-cell RNA-seq survey of the developmental landscape of the human prefrontal cortex. |
Nature |
2018 |
Zhong S, Zhang S, Fan X, Wu Q, Yan L, Dong J, Zhang H, Li L, Sun L, Pan N, Xu X, Tang F, Zhang J, Qiao J, Wang X. |
|
|
PRJNA412220 |
scRNA |
Homo sapiens |
|
Healthy Control |
29622030 |
Mapping human pluripotent stem cell differentiation pathways using high throughput single-cell RNA-sequencing. |
Genome biology |
2018 |
Han X, Chen H, Huang D, Chen H, Fei L, Cheng C, Huang H, Yuan GC, Guo G. |
|
|
PRJNA420514 |
scRNA |
Homo sapiens |
Cord Blood |
Healthy Control |
28754679 |
Adaptive from Innate: Human IFN-γ+CD4+ T Cells Can Arise Directly from CXCL8-Producing Recent Thymic Emigrants in Babies and Adults. |
Journal of immunology (Baltimore, Md. : 1950) |
2017 |
Das A, Rouault-Pierre K, Kamdar S, Gomez-Tourino I, Wood K, Donaldson I, Mein CA, Bonnet D, Hayday AC, Gibbons DL. |
|
|
PRJNA330840 |
scRNA |
Homo sapiens |
Oocyte |
Healthy Control |
29025019 |
Differing molecular response of young and advanced maternal age human oocytes to IVM. |
Human reproduction (Oxford, England) |
2017 |
Reyes JM, Silva E, Chitwood JL, Schoolcraft WB, Krisher RL, Ross PJ. |
|
|
PRJNA377237 |
scRNA |
Homo sapiens |
Hepatoblasts,Ipscs,Normal Liver,Primary Hepatic Organoids,Primary Hepatocytes,Secondary Hepatic Organoids |
Healthy Control |
28878125 |
Human hepatic organoids for the analysis of human genetic diseases. |
JCI insight |
2017 |
Guan Y, Xu D, Garfin PM, Ehmer U, Hurwitz M, Enns G, Michie S, Wu M, Zheng M, Nishimura T, Sage J, Peltz G. |
|
|
PRJNA395390 |
scRNA |
Homo sapiens |
|
Healthy Control |
29657097 |
Single-Cell Transcriptomic Profiling of Pluripotent Stem Cell-Derived SCGB3A2+ Airway Epithelium. |
Stem cell reports |
2018 |
McCauley KB, Alysandratos KD, Jacob A, Hawkins F, Caballero IS, Vedaie M, Yang W, Slovik KJ, Morley M, Carraro G, Kook S, Guttentag SH, Stripp BR, Morrisey EE, Kotton DN. |
|
|
PRJNA407490 |
scRNA |
Homo sapiens |
Pancreatic Islet |
Healthy Control |
28694456 |
Single-cell transcriptomics of East-Asian pancreatic islets cells. |
Scientific reports |
2017 |
Dorajoo R, Ali Y, Tay VSY, Kang J, Samydurai S, Liu J, Boehm BO. |
|
|
PRJNA382566 |
scRNA |
Homo sapiens |
|
Type I Diabetes |
28566371 |
Single-Cell RNA Sequencing Reveals Expanded Clones of Islet Antigen-Reactive CD4+ T Cells in Peripheral Blood of Subjects with Type 1 Diabetes. |
Journal of immunology (Baltimore, Md. : 1950) |
2017 |
Cerosaletti K, Barahmand-Pour-Whitman F, Yang J, DeBerg HA, Dufort MJ, Murray SA, Israelsson E, Speake C, Gersuk VH, Eddy JA, Reijonen H, Greenbaum CJ, Kwok WW, Wambre E, Prlic M, Gottardo R, Nepom GT, Linsley PS. |
|
|
PRJNA379013 |
scRNA |
Homo sapiens |
Esophagus |
Esophageal Squamous Cell Carcinoma |
31638164 |
Population and single‑cell transcriptome analyses reveal diverse transcriptional changes associated with radioresistance in esophageal squamous cell carcinoma. |
International journal of oncology |
2019 |
Wu H, Yu J, Kong D, Xu Y, Zhang Z, Shui J, Li Z, Luo H, Wang K. |
|
|
PRJNA322604 |
scRNA |
Homo sapiens |
|
Healthy Control |
28445465 |
Assembly of functionally integrated human forebrain spheroids. |
Nature |
2017 |
Birey F, Andersen J, Makinson CD, Islam S, Wei W, Huber N, Fan HC, Metzler KRC, Panagiotakos G, Thom N, O'Rourke NA, Steinmetz LM, Bernstein JA, Hallmayer J, Huguenard JR, Paşca SP. |
|
|
PRJNA378657 |
scRNA |
Homo sapiens |
Human Liver Parenchymal Tissue |
Healthy Control |
31350390 |
Single cell analysis of human foetal liver captures the transcriptional profile of hepatobiliary hybrid progenitors. |
Nature communications |
2019 |
Segal JM, Kent D, Wesche DJ, Ng SS, Serra M, Oulès B, Kar G, Emerton G, Blackford SJI, Darmanis S, Miquel R, Luong TV, Yamamoto R, Bonham A, Jassem W, Heaton N, Vigilante A, King A, Sancho R, Teichmann S, Quake SR, Nakauchi H, Rashid ST. |
|
|
PRJNA540429 |
scRNA |
Homo sapiens |
|
Healthy Control |
31543471 |
Single-Cell RNA Sequencing of hESC-Derived 3D Retinal Organoids Reveals Novel Genes Regulating RPC Commitment in Early Human Retinogenesis. |
Stem cell reports |
2019 |
Mao X, An Q, Xi H, Yang XJ, Zhang X, Yuan S, Wang J, Hu Y, Liu Q, Fan G. |
|
|
PRJNA506404 |
scRNA |
Homo sapiens |
|
Healthy Control |
31474513 |
Single-Cell Analysis of Human Mononuclear Phagocytes Reveals Subset-Defining Markers and Identifies Circulating Inflammatory Dendritic Cells. |
Immunity |
2019 |
Dutertre CA, Becht E, Irac SE, Khalilnezhad A, Narang V, Khalilnezhad S, Ng PY, van den Hoogen LL, Leong JY, Lee B, Chevrier M, Zhang XM, Yong PJA, Koh G, Lum J, Howland SW, Mok E, Chen J, Larbi A, Tan HKK, Lim TKH, Karagianni P, Tzioufas AG, Malleret B, Brody J, Albani S, van Roon J, Radstake T, Newell EW, Ginhoux F. |
|
|
PRJNA548370 |
scRNA |
Homo sapiens |
Primary Papillary Dermis,Primary Reticular Dermis |
Healthy Control |
29391249 |
Spatial and Single-Cell Transcriptional Profiling Identifies Functionally Distinct Human Dermal Fibroblast Subpopulations. |
The Journal of investigative dermatology |
2018 |
Philippeos C, Telerman SB, Oulès B, Pisco AO, Shaw TJ, Elgueta R, Lombardi G, Driskell RR, Soldin M, Lynch MD, Watt FM. |
|
|
PRJNA432084 |
scRNA |
Homo sapiens |
Heart |
Healthy Control |
30759401 |
Single-Cell Transcriptome Analysis Maps the Developmental Track of the Human Heart. |
Cell reports |
2019 |
Cui Y, Zheng Y, Liu X, Yan L, Fan X, Yong J, Hu Y, Dong J, Li Q, Wu X, Gao S, Li J, Wen L, Qiao J, Tang F. |
|
|
PRJNA415637 |
scRNA |
Homo sapiens |
Bone Marrow |
Healthy Control |
31561267 |
Single-cell RNA sequencing reveals chemokine self-feeding of myeloma cells promotes extramedullary metastasis. |
FEBS letters |
2020 |
Geng S, Wang J, Zhang X, Zhang JJ, Wu F, Pang Y, Zhong Y, Wang J, Wang W, Lyu X, Huang Y, Jing H. |
|
|
PRJNA565895 |
scRNA |
Homo sapiens |
Cerebrospinal Fluid (CSF) |
Autoimmune Encephalitis,Clinically Definite Multiple Sclerosis,Healthy Control,Subclinical Neuro-Inflammation |
31566584 |
Early adaptive immune activation detected in monozygotic twins with prodromal multiple sclerosis. |
The Journal of clinical investigation |
2019 |
Beltrán E, Gerdes LA, Hansen J, Flierl-Hecht A, Krebs S, Blum H, Ertl-Wagner B, Barkhof F, Kümpfel T, Hohlfeld R, Dornmair K. |
|
|
PRJNA513835 |
scRNA |
Homo sapiens |
|
Healthy Control |
28673540 |
Single-Cell Alternative Splicing Analysis with Expedition Reveals Splicing Dynamics during Neuron Differentiation. |
Molecular cell |
2017 |
Song Y, Botvinnik OB, Lovci MT, Kakaradov B, Liu P, Xu JL, Yeo GW. |
|
|
PRJNA339740 |
scRNA |
Homo sapiens |
|
Healthy Control |
28457750 |
Single-Cell RNA-Seq Analysis Maps Development of Human Germline Cells and Gonadal Niche Interactions. |
Cell stem cell |
2017 |
Li L, Dong J, Yan L, Yong J, Liu X, Hu Y, Fan X, Wu X, Guo H, Wang X, Zhu X, Li R, Yan J, Wei Y, Zhao Y, Wang W, Ren Y, Yuan P, Yan Z, Hu B, Guo F, Wen L, Tang F, Qiao J. |
|
|
PRJNA340388 |
scRNA |
Homo sapiens |
|
Healthy Control |
28061811 |
The nature and nurture of cell heterogeneity: accounting for macrophage gene-environment interactions with single-cell RNA-Seq. |
BMC genomics |
2017 |
Wills QF, Mellado-Gomez E, Nolan R, Warner D, Sharma E, Broxholme J, Wright B, Lockstone H, James W, Lynch M, Gonzales M, West J, Leyrat A, Padilla-Parra S, Filippi S, Holmes C, Moore MD, Bowden R. |
|
|
PRJNA348691 |
scRNA |
Homo sapiens |
|
Healthy Control |
27989770 |
Human Naive Pluripotent Stem Cells Model X Chromosome Dampening and X Inactivation. |
Cell stem cell |
2017 |
Sahakyan A, Kim R, Chronis C, Sabri S, Bonora G, Theunissen TW, Kuoy E, Langerman J, Clark AT, Jaenisch R, Plath K. |
|
|
PRJNA343935 |
scRNA |
Homo sapiens |
Placenta |
Healthy Control |
28174237 |
Single-cell transcriptomics of the human placenta: inferring the cell communication network of the maternal-fetal interface. |
Genome research |
2017 |
Pavličev M, Wagner GP, Chavan AR, Owens K, Maziarz J, Dunn-Fletcher C, Kallapur SG, Muglia L, Jones H. |
|
|
PRJNA345620 |
scRNA |
Homo sapiens |
Placenta |
Healthy Control |
30042384 |
Single-cell RNA-seq reveals the diversity of trophoblast subtypes and patterns of differentiation in the human placenta. |
Cell research |
2018 |
Liu Y, Fan X, Wang R, Lu X, Dang YL, Wang H, Lin HY, Zhu C, Ge H, Cross JC, Wang H. |
|
|
PRJNA352390 |
scRNA |
Homo sapiens |
Brain |
Healthy Control |
29867213 |
Spatial transcriptomic survey of human embryonic cerebral cortex by single-cell RNA-seq analysis. |
Cell research |
2018 |
Fan X, Dong J, Zhong S, Wei Y, Wu Q, Yan L, Yong J, Sun L, Wang X, Zhao Y, Wang W, Yan J, Wang X, Qiao J, Tang F. |
|
|
PRJNA406826 |
scRNA |
Homo sapiens |
Testis |
Non-Obstructive Azoospermia,Normal Fertility Or Obstructive Azoospermia (Normal Spermatogenesis) |
30174296 |
Single-Cell RNA Sequencing Analysis Reveals Sequential Cell Fate Transition during Human Spermatogenesis. |
Cell stem cell |
2018 |
Wang M, Liu X, Chang G, Chen Y, An G, Yan L, Gao S, Xu Y, Cui Y, Dong J, Chen Y, Fan X, Hu Y, Song K, Zhu X, Gao Y, Yao Z, Bian S, Hou Y, Lu J, Wang R, Fan Y, Lian Y, Tang W, Wang Y, Liu J, Zhao L, Wang L, Liu Z, Yuan R, Shi Y, Hu B, Ren X, Tang F, Zhao XY, Qiao J. |
|
|
PRJNA417066 |
scRNA |
Homo sapiens |
Neural Retina,Retinal Pigment Epithelium |
Healthy Control |
31269016 |
Dissecting the transcriptome landscape of the human fetal neural retina and retinal pigment epithelium by single-cell RNA-seq analysis. |
PLoS biology |
2019 |
Hu Y, Wang X, Hu B, Mao Y, Chen Y, Yan L, Yong J, Dong J, Wei Y, Wang W, Wen L, Qiao J, Tang F. |
|
|
PRJNA420849 |
scRNA |
Homo sapiens |
Kidney |
Healthy Control |
30257215 |
Dissecting the Global Dynamic Molecular Profiles of Human Fetal Kidney Development by Single-Cell RNA Sequencing. |
Cell reports |
2018 |
Wang P, Chen Y, Yong J, Cui Y, Wang R, Wen L, Qiao J, Tang F. |
|
|
PRJNA431200 |
scRNA |
Homo sapiens |
|
Healthy Control |
30548510 |
Deconstructing Retinal Organoids: Single Cell RNA-Seq Reveals the Cellular Components of Human Pluripotent Stem Cell-Derived Retina. |
Stem cells (Dayton, Ohio) |
2019 |
Collin J, Queen R, Zerti D, Dorgau B, Hussain R, Coxhead J, Cockell S, Lako M. |
|
|
PRJNA490648 |
scRNA |
Homo sapiens |
|
Healthy Control |
32049009 |
Transcriptional Programs Define Intratumoral Heterogeneity of Ewing Sarcoma at Single-Cell Resolution. |
Cell reports |
2020 |
Aynaud MM, Mirabeau O, Gruel N, Grossetête S, Boeva V, Durand S, Surdez D, Saulnier O, Zaïdi S, Gribkova S, Fouché A, Kairov U, Raynal V, Tirode F, Grünewald TGP, Bohec M, Baulande S, Janoueix-Lerosey I, Vert JP, Barillot E, Delattre O, Zinovyev A. |
|
|
PRJNA533606 |
scRNA |
Homo sapiens |
Left Colon,Liver,Lymph,Right Colon |
Colorectal Cancer |
30498128 |
Single-cell multiomics sequencing and analyses of human colorectal cancer. |
Science (New York, N.Y.) |
2018 |
Bian S, Hou Y, Zhou X, Li X, Yong J, Wang Y, Wang W, Yan J, Hu B, Guo H, Wang J, Gao S, Mao Y, Dong J, Zhu P, Xiu D, Yan L, Wen L, Qiao J, Tang F, Fu W. |
|
|
PRJNA382695 |
scRNA |
Oryza sativa |
Shoot |
|
31417977 |
Network-based feature selection reveals substructures of gene modules responding to salt stress in rice. |
Plant direct |
2019 |
Du Q, Campbell M, Yu H, Liu K, Walia H, Zhang Q, Zhang C. |
|
|
PRJNA385135 |
bulk |
Oryza sativa |
Shoot |
|
32513103 |
Characterization of the transcriptional divergence between the subspecies of cultivated rice (Oryza sativa). |
BMC genomics |
2020 |
Campbell MT, Du Q, Liu K, Sharma S, Zhang C, Walia H. |
|
|
PRJNA385135 |
bulk |
Oryza sativa cv Amaroo |
Coleoptile,Embryo,Germinating embryo |
|
27859855 |
Dynamic and rapid changes in the transcriptome and epigenome during germination and in developing rice (Oryza sativa) coleoptiles under anoxia and re-oxygenation. |
The Plant journal : for cell and molecular biology |
2017 |
Narsai R, Secco D, Schultz MD, Ecker JR, Lister R, Whelan J. |
|
|
PRJNA474721 |
bulk |
Oryza sativa |
Leaf |
|
31959799 |
Rice pyramided line IRBB67 (Xa4/Xa7) homeostasis under combined stress of high temperature and bacterial blight. |
Scientific reports |
2020 |
Dossa GS, Quibod I, Atienza-Grande G, Oliva R, Maiss E, Vera Cruz C, Wydra K. |
|
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PRJNA314700 |
bulk |
Oryza sativa Japonica Group |
Leaf,Seedling leaf (no root or endosperm) |
|
30253806 |
Dynamics and functional interplay of histone lysine butyrylation, crotonylation, and acetylation in rice under starvation and submergence. |
Genome biology |
2018 |
Lu Y, Xu Q, Liu Y, Yu Y, Cheng ZY, Zhao Y, Zhou DX. |
|
|
PRJNA436566 |
bulk |
Oryza sativa Japonica Group |
Leaf of seedling,Panicle of seedling,Root of seedling,Seedling |
|
29265542 |
Stress-responsive regulation of long non-coding RNA polyadenylation in Oryza sativa. |
The Plant journal : for cell and molecular biology |
2018 |
Yuan J, Li J, Yang Y, Tan C, Zhu Y, Hu L, Qi Y, Lu ZJ. |
|
|
PRJNA340947 |
bulk |
Oryza sativa Indica Group |
Leaf |
|
29314052 |
OsPRR37 confers an expanded regulation of the diurnal rhythms of the transcriptome and photoperiodic flowering pathways in rice. |
Plant, cell & environment |
2018 |
Liu C, Qu X, Zhou Y, Song G, Abiri N, Xiao Y, Liang F, Jiang D, Hu Z, Yang D. |
|
|
PRJNA469460 |
bulk |
Oryza sativa Japonica Group |
2nd leaf,Flag leaf |
|
28821707 |
Molecular bases for differential aging programs between flag and second leaves during grain-filling in rice. |
Scientific reports |
2017 |
Lee S, Jeong H, Lee S, Lee J, Kim SJ, Park JW, Woo HR, Lim PO, An G, Nam HG, Hwang D. |
|
|
PRJNA350792 |
bulk |
Oryza sativa Japonica Group |
Shoot |
|
29094353 |
Rice SUB1A constrains remodelling of the transcriptome and metabolome during submergence to facilitate post-submergence recovery. |
Plant, cell & environment |
2018 |
Locke AM, Barding GA, Sathnur S, Larive CK, Bailey-Serres J. |
|
|
PRJNA397883 |
bulk |
Glycine soja |
Seed |
|
28653111 |
Seed weight differences between wild and domesticated soybeans are associated with specific changes in gene expression. |
Plant cell reports |
2017 |
Yu C, Qu Z, Zhang Y, Zhang X, Lan T, Adelson DL, Wang D, Zhu Y. |
|
|
PRJNA369483 |
bulk |
Glycine max |
Seed |
|
24755115 |
Identification and characterization of transcript polymorphisms in soybean lines varying in oil composition and content. |
BMC genomics |
2014 |
Goettel W, Xia E, Upchurch R, Wang ML, Chen P, An YQ. |
|
|
PRJNA242863 |
bulk |
Glycine max |
Seed |
|
26678836 |
Genome-wide transcriptome analyses of developing seeds from low and normal phytic acid soybean lines. |
BMC genomics |
2015 |
Redekar NR, Biyashev RM, Jensen RV, Helm RF, Grabau EA, Maroof MA. |
|
|
PRJNA304631 |
bulk |
Glycine max |
Seedling cotyledon |
|
25070765 |
Transcription factors and glyoxylate cycle genes prominent in the transition of soybean cotyledons to the first functional leaves of the seedling. |
Functional & integrative genomics |
2014 |
Shamimuzzaman M, Vodkin L. |
|
|
PRJNA182292 |
bulk |
Glycine max |
Seedling cotyledon |
|
25635113 |
Direct detection of transcription factors in cotyledons during seedling development using sensitive silicon-substrate photonic crystal protein arrays. |
Plant physiology |
2015 |
Jones SI, Tan Y, Shamimuzzaman M, George S, Cunningham BT, Vodkin L. |
|
|
PRJNA182292 |
bulk |
Glycine max |
Cotyledon,Seed coat,Whole seed |
|
23555009 |
Using RNA-Seq to profile soybean seed development from fertilization to maturity. |
PloS one |
2013 |
Jones SI, Vodkin LO. |
|
|
PRJNA184365 |
bulk |
Glycine max |
Pod |
|
31456133 |
Pod-shattering characteristics differences between two groups of soybeans are associated with specific changes in gene expression. |
Functional & integrative genomics |
2020 |
Kang X, Cai J, Chen Y, Yan Y, Yang S, He R, Wang D, Zhu Y. |
|
|
PRJNA533590 |
bulk |
Glycine max |
Leaf |
|
31757957 |
Glycerol-3-phosphate mediates rhizobia-induced systemic signaling in soybean. |
Nature communications |
2019 |
Shine MB, Gao QM, Chowda-Reddy RV, Singh AK, Kachroo P, Kachroo A. |
|
|
PRJNA579169 |
bulk |
Glycine max |
Seedling |
|
26689712 |
Transcriptome profiling of soybean (Glycine max) roots challenged with pathogenic and non-pathogenic isolates of Fusarium oxysporum. |
BMC genomics |
2015 |
Lanubile A, Muppirala UK, Severin AJ, Marocco A, Munkvold GP. |
|
|
PRJNA278121 |
bulk |
Glycine max |
Whole root |
|
31341170 |
Transcriptome profiling of interaction effects of soybean cyst nematodes and soybean aphids on soybean. |
Scientific data |
2019 |
Neupane S, Mathew FM, Varenhorst AJ, Nepal MP. |
|
|
PRJNA514200 |
bulk |
Glycine max |
Leaf |
|
26350764 |
Identification of Soybean Proteins and Genes Differentially Regulated in Near Isogenic Lines Differing in Resistance to Aphid Infestation. |
Journal of proteome research |
2015 |
Brechenmacher L, Nguyen TH, Zhang N, Jun TH, Xu D, Mian MA, Stacey G. |
|
|
PRJNA280872 |
bulk |
Glycine max |
Leaf |
|
31182145 |
Transcriptome profiling of induced susceptibility effects on soybean-soybean aphid (Hemiptera: Aphididae) interaction. |
BMC research notes |
2019 |
Neupane S, Varenhorst AJ, Nepal MP. |
|
|
PRJNA530958 |
bulk |
Glycine max |
First trifoliate true leaf |
|
30041471 |
Early Transcriptomic Response to Phosphate Deprivation in Soybean Leaves as Revealed by RNA-Sequencing. |
International journal of molecular sciences |
2018 |
Zeng H, Zhang X, Zhang X, Pi E, Xiao L, Zhu Y. |
|
|
PRJNA412240 |
bulk |
Glycine max |
Nodule |
|
30261621 |
Genome Wide Transcriptome Analysis Reveals Complex Regulatory Mechanisms Underlying Phosphate Homeostasis in Soybean Nodules. |
International journal of molecular sciences |
2018 |
Xue Y, Zhuang Q, Zhu S, Xiao B, Liang C, Liao H, Tian J. |
|
|
PRJNA479468 |
bulk |
Sorghum bicolor |
Male gametophyte |
|
31964983 |
Transcriptional trajectories of anther development provide candidates for engineering male fertility in sorghum. |
Scientific reports |
2020 |
Dhaka N, Krishnan K, Kandpal M, Vashisht I, Pal M, Sharma MK, Sharma R. |
|
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PRJNA591805 |
bulk |
Sorghum bicolor |
First axillary bud |
|
30875440 |
Sorghum tiller bud growth is repressed by contact with the overlying leaf. |
Plant, cell & environment |
2019 |
Liu R, Finlayson SA. |
|
|
PRJNA525462 |
bulk |
Sorghum bicolor |
Leaf,Root |
|
31806758 |
Transcriptomic analysis of field-droughted sorghum from seedling to maturity reveals biotic and metabolic responses. |
Proceedings of the National Academy of Sciences of the United States of America |
2019 |
Varoquaux N, Cole B, Gao C, Pierroz G, Baker CR, Patel D, Madera M, Jeffers T, Hollingsworth J, Sievert J, Yoshinaga Y, Owiti JA, Singan VR, DeGraaf S, Xu L, Blow MJ, Harrison MJ, Visel A, Jansson C, Niyogi KK, Hutmacher R, Coleman-Derr D, O'Malley RC, Taylor JW, Dahlberg J, Vogel JP, Lemaux PG, Purdom E. |
|
|
PRJNA527782 |
bulk |
Sorghum bicolor |
Root |
|
24597475 |
Identification of differentially expressed genes between sorghum genotypes with contrasting nitrogen stress tolerance by genome-wide transcriptional profiling. |
BMC genomics |
2014 |
Gelli M, Duo Y, Konda AR, Zhang C, Holding D, Dweikat I. |
|
|
PRJNA237453 |
bulk |
Triticum aestivum |
Leaf,Stem |
|
30778362 |
The Impact of the Wheat Rht-B1b Semi-Dwarfing Allele on Photosynthesis and Seed Development Under Field Conditions. |
Frontiers in plant science |
2019 |
Jobson EM, Johnston RE, Oiestad AJ, Martin JM, Giroux MJ. |
|
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PRJNA514367 |
bulk |
Triticum aestivum |
Embryo,Endorsperm,Seed coat |
|
31628162 |
The Transcriptional Landscape of Polyploid Wheats and Their Diploid Ancestors during Embryogenesis and Grain Development. |
The Plant cell |
2019 |
Xiang D, Quilichini TD, Liu Z, Gao P, Pan Y, Li Q, Nilsen KT, Venglat P, Esteban E, Pasha A, Wang Y, Wen R, Zhang Z, Hao Z, Wang E, Wei Y, Cuthbert R, Kochian LV, Sharpe A, Provart N, Weijers D, Gillmor CS, Pozniak C, Datla R. |
|
|
PRJNA532455 |
bulk |
Triticum aestivum |
Coleoptile |
|
30804501 |
A linear nonribosomal octapeptide from Fusarium graminearum facilitates cell-to-cell invasion of wheat. |
Nature communications |
2019 |
Jia LJ, Tang HY, Wang WQ, Yuan TL, Wei WQ, Pang B, Gong XM, Wang SF, Li YJ, Zhang D, Liu W, Tang WH. |
|
|
PRJNA483762 |
bulk |
Oryza sativa Japonica Group |
Root,Shoot |
|
24249833 |
Spatio-temporal transcript profiling of rice roots and shoots in response to phosphate starvation and recovery. |
The Plant cell |
2013 |
Secco D, Jabnoune M, Walker H, Shou H, Wu P, Poirier Y, Whelan J. |
|
|
PRJNA215013 |
bulk |
Oryza sativa Japonica Group |
Anther,Pistil,Seed,Shoot |
|
25517485 |
Genome-wide screening and functional analysis identify a large number of long noncoding RNAs involved in the sexual reproduction of rice. |
Genome biology |
2014 |
Zhang YC, Liao JY, Li ZY, Yu Y, Zhang JP, Li QF, Qu LH, Shu WS, Chen YQ. |
|
|
PRJNA262032 |
bulk |
Oryza sativa Japonica Group |
Root,Shoot |
|
24816929 |
Genome-wide transcriptome analysis reveals that cadmium stress signaling controls the expression of genes in drought stress signal pathways in rice. |
PloS one |
2014 |
Oono Y, Yazawa T, Kawahara Y, Kanamori H, Kobayashi F, Sasaki H, Mori S, Wu J, Handa H, Itoh T, Matsumoto T. |
|
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PRJDB2154 |
bulk |
Oryza sativa Japonica Group |
Panicle |
|
24577842 |
Genome-wide disruption of gene expression in allopolyploids but not hybrids of rice subspecies. |
Molecular biology and evolution |
2014 |
Xu C, Bai Y, Lin X, Zhao N, Hu L, Gong Z, Wendel JF, Liu B. |
|
|
PRJNA234333 |
bulk |
Oryza sativa Japonica Group |
Shoot |
|
25002488 |
Mutation of a major CG methylase in rice causes genome-wide hypomethylation, dysregulated genome expression, and seedling lethality. |
Proceedings of the National Academy of Sciences of the United States of America |
2014 |
Hu L, Li N, Xu C, Zhong S, Lin X, Yang J, Zhou T, Yuliang A, Wu Y, Chen YR, Cao X, Zemach A, Rustgi S, von Wettstein D, Liu B. |
|
|
PRJNA253163 |
bulk |
Oryza sativa Japonica Group |
Anther |
|
24635777 |
Rice germline-specific Argonaute MEL1 protein binds to phasiRNAs generated from more than 700 lincRNAs. |
The Plant journal : for cell and molecular biology |
2014 |
Komiya R, Ohyanagi H, Niihama M, Watanabe T, Nakano M, Kurata N, Nonomura K. |
|
|
PRJDB2204 |
bulk |
Oryza sativa Japonica Group |
Callus,Leaf,Panicle,Root,Seed,Shoot |
|
22042334 |
Retrogenes in rice (Oryza sativa L. ssp. japonica) exhibit correlated expression with their source genes. |
Genome biology and evolution |
2011 |
Sakai H, Mizuno H, Kawahara Y, Wakimoto H, Ikawa H, Kawahigashi H, Kanamori H, Matsumoto T, Itoh T, Gaut BS. |
|
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PRJDA67119 |
bulk |
Oryza sativa Japonica Group, Oryza sativa Indica Group |
Root,Shoot |
|
23857470 |
Diversity in the complexity of phosphate starvation transcriptomes among rice cultivars based on RNA-Seq profiles. |
Plant molecular biology |
2013 |
Oono Y, Kawahara Y, Yazawa T, Kanamori H, Kuramata M, Yamagata H, Hosokawa S, Minami H, Ishikawa S, Wu J, Antonio B, Handa H, Itoh T, Matsumoto T. |
|
|
PRJDB2658 |
bulk |
Oryza sativa Japonica Group |
Root,Shoot |
|
22537016 |
Comparative transcriptome analysis of transporters, phytohormone and lipid metabolism pathways in response to arsenic stress in rice (Oryza sativa). |
The New phytologist |
2012 |
Yu LJ, Luo YF, Liao B, Xie LJ, Chen L, Xiao S, Li JT, Hu SN, Shu WS. |
|
|
PRJNA153619 |
bulk |
Oryza sativa Japonica Group |
Above-ground tissue of seedling,Whole tissue of above-ground seedling |
|
26243209 |
Loss of function mutations in the rice chromomethylase OsCMT3a cause a burst of transposition. |
The Plant journal : for cell and molecular biology |
2015 |
Cheng C, Tarutani Y, Miyao A, Ito T, Yamazaki M, Sakai H, Fukai E, Hirochika H. |
|
|
PRJNA263691 |
bulk |
Oryza sativa Japonica Group |
Leaf |
|
26257749 |
TAL effectors and activation of predicted host targets distinguish Asian from African strains of the rice pathogen Xanthomonas oryzae pv. oryzicola while strict conservation suggests universal importance of five TAL effectors. |
Frontiers in plant science |
2015 |
Wilkins KE, Booher NJ, Wang L, Bogdanove AJ. |
|
|
PRJNA280380 |
bulk |
Oryza sativa Japonica Group |
Leaf |
|
26821568 |
A transcription activator-like effector from Xanthomonas oryzae pv. oryzicola elicits dose-dependent resistance in rice. |
Molecular plant pathology |
2017 |
Hummel AW, Wilkins KE, Wang L, Cernadas RA, Bogdanove AJ. |
|
|
PRJNA281369 |
bulk |
Oryza sativa Japonica Group |
Root |
|
26196146 |
Stress induced gene expression drives transient DNA methylation changes at adjacent repetitive elements. |
eLife |
2015 |
Secco D, Wang C, Shou H, Schultz MD, Chiarenza S, Nussaume L, Ecker JR, Whelan J, Lister R. |
|
|
PRJNA291004 |
bulk |
Glycine max |
|
|
32553274 |
Pan-Genome of Wild and Cultivated Soybeans. |
Cell |
2020 |
Liu Y, Du H, Li P, Shen Y, Peng H, Liu S, Zhou GA, Zhang H, Liu Z, Shi M, Huang X, Li Y, Zhang M, Wang Z, Zhu B, Han B, Liang C, Tian Z. |
|
|
PRJCA002030 |
bulk |