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Species Tissue Disease Pubmed ID Title Journal Year Author Corresponding Author Institution of Corresponding Author Project ID Bulk/scRNA
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