National Genomics Data Center

BIG Search

BIG Search is a scalable text search engine built based on ElasticSearch (a highly scalable open-source full-text search and analytics engine based on Apache Lucene). It features cross-domain search and facilitates users to gain access to a wide range of biomedical data, not only from NGDC databases but also partner databases throughout the world.

e.g., PRJCA000126;SAMC000385;tp53;EGFR; human; KaKs_Calculator

Total 183 record(s) from BioProject

BioProject: Bisulfite Free Nanoscale Analysis of Hydroxymethylcytosine at Single Base Resolution

  • Accession: PRJCA002841
  • Title: Bisulfite Free Nanoscale Analysis of Hydroxymethylcytosine at Single Base Resolution
  • Description: High-resolution detection of genome-wide 5-hydroxymethylcytosine (5hmC) sites of small-scale samples remains challenging. Here, we present hmC- CATCH, a bisulfite-free, base-resolution method for the genome-wide detection of 5hmC. hmC-CATCH is based on selective 5hmC oxidation, chemical labeling and subsequent C-to-T transition during PCR. Requiring only nanoscale input genomic DNA samples, hmC- CATCH enabled us to detect genome-wide hydroxyme- thylome of human embryonic stem cells in a cost-effective manner. Further application of hmC-CATCH to cell-free DNA (cfDNA) of healthy donors and cancer patients revealed base-resolution hydroxymethylome in the human cfDNA for the first time. We anticipate that our chemical biology approach will find broad applications in hydroxymethylome analysis of limited biological and clinical samples.
  • Samples: SAMC194111 SAMC194110 SAMC194109 SAMC194108 SAMC194107 SAMC194106 more
  • GSAs: CRA002801
  • BasicInfo : PRJCA002841; Epigenomics; Medical

BioProject: RNA-seq of HUVECs

  • Accession: PRJCA003093
  • Title: RNA-seq of HUVECs
  • Description: Primary human umbilical vein endothelial cells (HUVECs) infected with pri-miR-218-1 or control adenovirus for 48 h were used for mRNA sequencing. RNA was extracted, sequenced, and analyzed by custom service provided by Megagenomics using an Illumina HiSeq3000.
  • Samples: SAMC200868 SAMC200873 SAMC200872 SAMC200871 SAMC200870 SAMC200869
  • BasicInfo : PRJCA003093; Transcriptome or Gene expression Raw sequence reads; Medical

BioProject: Selenium deficiency-induced redox imbalance leads to metabolic reprogramming and inflammation in liver

  • Accession: PRJCA002073
  • Title: Selenium deficiency-induced redox imbalance leads to metabolic reprogramming and inflammation in liver
  • Description: The interplay of selenium (Se), redox homeostasis, and energy metabolism is related to many human metabolic diseases. To explore the underlying mechanisms of suboptimal Se induced liver diseases, we fed pure line pigs with a Se deficiency diet (0.007 mg/kg) for 16 weeks, studied how hepatic metabolome (hydrophilic and lipophilic), global proteome, and whole-transcriptome response to, and identified molecules and pathways involved in. Se deficiency decreased hair, blood, and hepatic Se contents, decreased blood and hepatic anti-oxidant capacity and increased ROS and pro-inflammatory factors levels, and induced lymphocytes infiltration, stripe-like hyperplasia, and sinus expansion in liver. Se deficiency triggered hepatic oxidative stress by down regulating selenoproteins at genes mRNA and protein levels, hindering glutathione system, along with an enhanced glutathione synthesis and catabolism as substrates were decreased and mRNA expression of enzymes involved in were up-regulated. A Warburg effect was observed, as glycolysis were enhanced and significant amounts of glycolytic metabolites were diverted into phosphate pentose pathway for production of NADPH. The TCA cycle was disfunction as the preliminary metabolites were decreased, while glutamine, malic acid, and fumarate were increased, showing that TCA cycle was shifted to a glutamine catabolism preferred mode, rather than using glycolysis origin substrates. The reprogrammed central carbon metabolism also brought out a widely reduction of lipid synthesis. Also, Se deficiency initiating inflammation by activating NF-κB pathway through multiple mechanisms. These results generated a comprehensive picture of the essential physiological role of Se in liver health, which may provide intervention targets for Se deficiency-induced disease in the future.
  • Samples: SAMC126283 SAMC126282 SAMC126281 SAMC126280 SAMC126279 SAMC126278 more
  • GSAs: CRA002242 CRA002241
  • BasicInfo : PRJCA002073; Transcriptome or Gene expression Raw sequence reads TMT 10-plex proteomics data; Nutriton and Health

BioProject: A Severe Case of Rickettsia sibirica str. BJ-90 Identified by Metagenomic Sequencing in Qinghai, China

  • Accession: PRJCA002879
  • Title: A Severe Case of Rickettsia sibirica str. BJ-90 Identified by Metagenomic Sequencing in Qinghai, China
  • Description: Identification of the first human rickettsioses from Qinghai-Tibet plateau by metagenomic sequencing, amplicon sequencing and serological examination
  • Samples: SAMC196048
  • GSAs: CRA002872
  • BasicInfo : PRJCA002879; Raw sequence reads; Medical

BioProject: Oral and intestinal microbiota of Xianyang Han populations

  • Accession: PRJCA002832
  • Title: Oral and intestinal microbiota of Xianyang Han populations
  • Description: Diet, environment, and genomic context exert a significant impact on the oral and gut microbiota of humans. Migration may be accompanied by changes in human eating habits and living environment, then could affecting oral and gut flora. To understand the association of oral microbiota, gut microbiota and migration, we collected saliva samples and stool samples from 77 Xianyang Han populations, and analyzed the diversity and richness of oral and intestinal microbiota.
  • Samples: SAMC192630 SAMC192672 SAMC192671 SAMC192670 SAMC192669 SAMC192668 more
  • GSAs: CRA002780
  • BasicInfo : PRJCA002832; Metagenome; Medical

BioProject: High-throughput RNA sequencing of trophoblast cell derived from different origin

  • Accession: PRJCA002798
  • Title: High-throughput RNA sequencing of trophoblast cell derived from different origin
  • Description: High throughput RNA sequencing of JEG3 cells after AP2 siRNA interfering, trophoblast cells conversion from human embryonic stem cells
  • BasicInfo : PRJCA002798; Raw sequence reads; Medical

BioProject: Ancient DNA indicates human population shifts and admixture in northern and southern China

  • Accession: PRJCA002264
  • Title: Ancient DNA indicates human population shifts and admixture in northern and southern China
  • Description: Present-day East Asians share a close relationship to each other but lack a well-established genetic history. We sequenced genome-wide SNPs from 26 individuals spanning a period of 9,500-300 years ago from East Asia, overlapping the Neolithic period in China. These data support that ancient East Asians are closest to today's East Asians and are divergent from ancient Southeast Asian hunter-gatherers. Furthermore, Neolithic East Asians show higher genetic differentiation than today's East Asians, likely due to increased gene flow, particularly of northern East Asian ancestry into southern East Asia. Ancestry associated with Neolithic southern East Asians from the mainland is closest to Austronesians, indicating a proto-Austronesian origin mainland southern China. Overall, modern East Asian genetics have been impacted by both northern and southern East Asians since 9,500 years ago.
  • BasicInfo : PRJCA002264; Phenotype or Genotype Genome sequencing ; Evolution

BioProject: A Single-Cell Transcriptomic Atlas of Arterial Aging in Cynomolgus Monkey

  • Accession: PRJCA002454
  • Title: A Single-Cell Transcriptomic Atlas of Arterial Aging in Cynomolgus Monkey
  • Description: Our understanding of how human aging affects the cellular and molecular components of the vasculature and contributes to cardiovascular diseases is still limited. Here we reported a single-cell transcriptomic survey of aortic arches and coronary arteries in young and old cynomolgus monkeys. Our data defined the molecular signatures of specialized arteries and identified eight novel markers discriminating aortic and coronary vasculature. Gene network analyses characterized transcriptional landmarks that regulate vascular senility and positioned FOXO3A, a longevity-associated transcription factor, as a master regulator gene that was downregulated in six subtypes of monkey vascular cells during aging. Targeted inactivation of FOXO3A in human vascular endothelial cells recapitulated the major phenotypic defects observed in aged monkey arteries, verifying FOXO3A as a functional geroprotective factor in arterial endothelial cells. Our study provides a critical resource for understanding the principles underlying arterial aging and contributes important clues to future treatment of age-associated vascular disorders.
  • Samples: SAMC151004 SAMC151003 SAMC151002 SAMC151001 SAMC151000 SAMC150999 more
  • GSAs: CRA002501 CRA002496
  • BasicInfo : PRJCA002454; Transcriptome or Gene expression Raw sequence reads Genome sequencing ; Model organism

BioProject: Mapping the spreading routes of lymphatic metastases in human colorectal cancer

  • Accession: PRJCA002408
  • Title: Mapping the spreading routes of lymphatic metastases in human colorectal cancer
  • Description: Lymph node metastases are frequently diagnosed in patients with colorectal cancer. However, the detailed disseminating routes of cancer cells within the lymphatic network remain largely unknown. Here, we analyzed the subclonal structure of 94 tumor samples from 10 CRC patients, covering almost all LNMs, as well as primary tumor and liver metastases. We portrayed the first lymphatic metastatic map for CRC.
  • BasicInfo : PRJCA002408; Exome; Medical

BioProject: Therapeutic potential of antimicrobial peptides in diseases of humans and animals

  • Accession: PRJCA002196
  • Title: Therapeutic potential of antimicrobial peptides in diseases of humans and animals
  • Description: Staphylococcus aureus is a facultative pathogen that can cause myriad infectious diseases in humans and animals, To investigate the effects of antimicrobial peptides on genes expression of S. aureus, transcriptome sequencing was performed.
  • Samples: SAMC134278 SAMC134279
  • GSAs: CRA002331
  • BasicInfo : PRJCA002196; Transcriptome or Gene expression; Medical