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Series GSE113606 Query DataSets for GSE113606
Status Public on Apr 24, 2019
Title RNA-seq and ATAC-seq analysis of the role of PBRM1 under stress conditions
Organisms Homo sapiens; Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary We used RNA-seq to characterize the contributions of PBRM1 to gene expression in NmuMG cells with and without oxidative or low-glucose stress conditions. Further, we used ATAC-seq to characterize the effects of PBRM1 on chromatin accessibility in HK-2 and NMuMG cell lines. Our analyses reveal a role for PBRM1 in expression of genes associated with stress responses and with specific transcription factor families, such as the FOXO family.
 
Overall design Libraries prepared for RNA-seq or ATAC-seq were sequenced using Illumina HiSeq technology. Sequencing was performed in biological triplicate.
 
Contributor(s) Dykhuizen E, Chowdhury B, Carter B
Citation(s) 31077944
Submission date Apr 24, 2018
Last update date May 29, 2019
Contact name Benjamin Carter
E-mail(s) beccarte@gmail.com
Organization name National Institutes of Health
Department NHLBI
Lab Keji Zhao
Street address 10 Center Drive
City Bethesda
State/province MD
ZIP/Postal code 20814
Country USA
 
Platforms (2)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
Samples (30)
GSM3110043 HK-2 ATAC-seq null replicate 1
GSM3110044 HK-2 ATAC-seq null replicate 2
GSM3110045 HK-2 ATAC-seq null replicate 3
Relations
BioProject PRJNA453373
SRA SRP142505

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE113606_ATAC_HK2_dec_HOMER.txt.gz 775.2 Kb (ftp)(http) TXT
GSE113606_ATAC_HK2_inc_HOMER.txt.gz 475.4 Kb (ftp)(http) TXT
GSE113606_ATAC_NMuMG_dec_HOMER.txt.gz 397.8 Kb (ftp)(http) TXT
GSE113606_ATAC_NMuMG_inc_HOMER.txt.gz 621.7 Kb (ftp)(http) TXT
GSE113606_RNA-seq_counts_matrix.txt.gz 863.9 Kb (ftp)(http) TXT
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Processed data are available on Series record

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