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Series GSE115438 Query DataSets for GSE115438
Status Public on Jun 07, 2018
Title Positional specificity of different transcription factor classes within enhancers
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Third-party reanalysis
Summary Gene expression is controlled by sequence-specific transcription factors (TFs), which bind to regulatory sequences in DNA. The degree to which the arrangement of motif sites within regulatory elements determines their function remains unclear. Here, we show that the positional distribution of TF motif sites within NDRs fall into six distinct classes. These patterns are highly consistent across cell types, and bring together factors that have similar functional and binding properties. Furthermore, the position of motif sites appears to be related to their known functions. Our results suggest TFs play distinct roles in forming a functional enhancer, facilitated by their position within a regulatory sequence.
Overall design ATAC-seq in two immune cell lines, Jurkat and U937.

H3K27ac ChIP-seq in two immune cell lines, Jurkat and U937, representing a re-analysis of SRR1057274 from sample GSM1296384 (Jurkat) and ERR671846 from sample ERS420369 (U937). We generated the following processed data files:
Contributor(s) Grossman SR
Citation(s) 29987030
Submission date Jun 06, 2018
Last update date Mar 26, 2019
Contact name Sharon R Grossman
Organization name Broad Institute
Street address 415 Main Street
City Cambridge
State/province MA
ZIP/Postal code 02142
Country USA
Platforms (1)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (2)
GSM3178273 Jurkat_ATAC_seq
GSM3178274 U937_ATAC-seq
Reanalysis of GSM1296384
BioProject PRJNA474957
SRA SRP149948

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
GSE115438_Jurkat-H3K27ac.gappedPeak.gz 1.6 Mb (ftp)(http) GAPPEDPEAK
GSE115438_RAW.tar 7.6 Mb (http)(custom) TAR (of NARROWPEAK)
GSE115438_U937-H3K27ac.gappedPeak.gz 239.2 Kb (ftp)(http) GAPPEDPEAK
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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