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Series GSE96800 Query DataSets for GSE96800
Status Public on Mar 29, 2017
Title Transcription and chromatin profiling in differentiating THP-1 monocytes and THP-1 derived macrophages
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Summary Here we profile nascent transcription, RNA polymerase III occupancy, chromatin accessibility, and H3K27ac levels in THP-1 monocytes and THP-1 derived macrophages after 72 hr exposure to phorbol myristate acetate (PMA).
 
Overall design Biotin-capture of nascent transcription, ChIP-seq against RNA polymerase III subunit RPC4 (POLR3D), histone H3K27 acetylation (H3K27ac), CCCTC-binding factor (CTCF), and MAF1, and ATAC-seq in THP-1 monocytes and THP-1 derived macrophages after 72 hr exposure to PMA.
 
Contributor(s) Van Bortle K, Phanstiel D, Snyder M
Citation(s) 28890333
Submission date Mar 19, 2017
Last update date May 15, 2019
Contact name Kevin Van Bortle
Organization name Stanford University
Department Genetics
Lab Michael Snyder
Street address 3165 Porter Dr
City Palo Alto
State/province CA
ZIP/Postal code 94043
Country USA
 
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (40)
GSM2544216 ATAC-seq_monocyte1a
GSM2544217 ATAC-seq_monocyte2a
GSM2544218 ATAC-seq_macrophage1a
Relations
BioProject PRJNA379744
SRA SRP102154

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
GSE96800_ATAC_peak_edgeR_raw.txt.gz 10.8 Mb (ftp)(http) TXT
GSE96800_CTCF_peak_edgeR_raw.txt.gz 4.2 Mb (ftp)(http) TXT
GSE96800_H3K27_peak_edgeR_raw.txt.gz 5.5 Mb (ftp)(http) TXT
GSE96800_MAF1_peaks_edgeR.txt.gz 414.5 Kb (ftp)(http) TXT
GSE96800_POLR3D_tDNA_counts.txt.gz 10.3 Kb (ftp)(http) TXT
GSE96800_PROseq_tDNA_counts.txt.gz 11.1 Kb (ftp)(http) TXT
GSE96800_RAW.tar 17.4 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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