#cngbdbproject

[blogibb-blog]

There raw data of 321 chicken cecal samples.

Data type: Metagenome Sample scope: Multispecies Submitter: Panpan Qin; BGI Release date: 2019-01-01 Updated: 2019-01-14 Statistic: Sample: 321, Experiments: 321, Runs: 321 Data size: 1.92 TB

[blogibb-blog]

This study is to identify downstream genes regulated by STAT3 in response cytosolic acidification. Dysregulated intracellular pH is emerging as a hallmark of cancer. In spite of their acidic environment, cancer cells maintain alkaline intracellular pH (≥7.4) that promotes cancer progression by inhibiting apoptosis and increasing glycolysis, cell growth, migration and invasion. Here, we identify signal transducer and activator of transcription 3 (STAT3) as a key player in the maintenance of alkaline cytosolic pH. STAT3 associates with the vacuolar H+-ATPase on lysosomal membranes in a coiled coil domain-dependent manner and increases its activity in living cells and in vitro. Accordingly, STAT3 depletion disrupts intracellular proton equilibrium by decreasing and increasing cytosolic and lysosomal pH, respectively. This dysregulation can be reverted by reconstitution with wild type STAT3 as well as STAT3 mutants unable to activate target genes (Tyr-705-Phe and DNA binding mutant) or to regulate mitochondrial respiration (Ser-727-Ala). Upon cytosolic acidification, phospho-Tyr-705-STAT3 is rapidly dephosphorylated, transcriptionally inactivated and further recruited to lysosomal membranes to reestablish intracellular proton equilibrium and to enhance cell survival. These data reveal STAT3 as a regulator of intracellular pH, and vice versa intracellular pH as a regulator of STAT3 localization and activity.

Data type: Raw sequence reads;  Transcriptome or Gene expression Sample scope: Multiisolate Relevance: Medical Submitter: jinrong huang; BGI Release date: 2018-10-10 Updated: 2018-09-10 Statistic: Sample: 12, Experiments: 12, Runs: 12 Data size: 19.67 GB

[blogibb-blog]

The study intended to search for susceptibility genes to mycobacterial diseases. Whole exome sequencing was performed on genomic DNA from patients who had suffered form mycobacterial diseases, either due to poorly virulent mycobacterial species (such as environmental mycobacteria or the BCG vaccine) or the more virulent Mycobacterium tuberculosis responsible for tuberculosis in humans. Data type: raw sequence reads

Sample scope: Multispecies Relevance: Medical Organization: Rockefeller University Accession in other database: PRJNA495387 Updated: 2018-10-09 DOI: 10.26036/CNPhis0002799 Statistic: Sample: 31, Experiments: 31, Runs: 31

[blogibb-blog]

Confirmation of HLA sequences using sanger sequencing data and validation of sequence analysis results using NGS data

Data type: Targeted Locus (Loci) Sample scope: Monoisolate Submitter: Bochen Cheng; University of Chinese Academy of Sciences Release date: 2019-01-26 Updated: 2019-01-23 Statistic: Sample: 1, Experiments: 1, Runs: 1 Data size: 1.3 GB

[blogibb-blog]

14 breast cancer exomes and matched transcriptomes generated from BGISEQ-500 sequencing platform.

Data type: Exome;  Map;  Transcriptome or Gene expression Sample scope: Multiisolate Submitter: BGI-Shenzhen Release date: 2019-04-30 Updated: 2019-03-06 Statistic: Sample: 204 Experiments: 204 Runs: 204

Data size: 4.83 TB

[blogibb-blog]

Noninvasive prenatal detection for pathogenic CNVs related with fetal monogenetic diseases using target region capture sequencing.

Data type: genome sequencing Sample scope: Monoisolate Relevance: Medical Organization: BGI-Shenzhen Accession in other database: PRJNA187139 Updated: 2013-01-24 DOI: 10.26036/CNPhis0000475 Statistic: Sample: 38 Experiments: 117 Runs: 130

[blogibb-blog]

Amniocentesis is a procedure that collects cells from the fetus to allow testing for abnormal chromosomes, altered chromosomal copy number, or a small number of genes that have small single to multi-base defects. However, it is blind to birth defects known to be caused by single to megabase scale changes in thousands of different genes and chromosomal regions. In an effort to improve the detection of the number of birth defects by this test we apply whole genome sequencing to 30 amniocentesis samples. For all samples cell free DNA (cfDNA), isolated from the amniotic fluid, and DNA isolated from the cell pellet, were sequenced to ~50X genome coverage using complete genomics nanoarray platform. In a subset of the samples, Long Fragment Read (LFR) libraries were generated from DNA isolated from cells and sequenced to ~100X genome coverage. DNA isolated from the blood of each parent was sequenced to ~50X on the same platform for all amniotic samples. In total... (for more see dbGaP study page.)

Data type: Phenotype or Genotype Sample scope: Multiisolate Relevance: Medical Organization: COMPLETE GENOMICS, INC. Accession in other database: PRJNA369591 DOI: 10.26036/CNPhis0000415 Statistic: Sample: 105 Experiments: 105 Runs: 105