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Series GSE87254 Query DataSets for GSE87254
Status Public on Jul 12, 2018
Title Trac-looping measures genome structure and chromatin accessibility
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Interaction between different chromatin regions plays critical roles in genome organization and regulation of transcription. Existing technologies of analyzing genome-wide chromatin interactions rely on in vitro proximity-based ligation of interacting chromatin fragments and thus are prone to potential artifacts. We now report a novel technique, Transposase-mediated Analysis of Chromatin loops (TrAC-loop), for detection of genome-wide chromatin interactions between regulatory regions. With this technique, a bivalent oligonucleotide linker is inserted between two interacting chromatin regions such that the distant interacting chromatin regions can be directly amplified by PCR and thus avoids the prior chromatin fragmentation and subsequent error-prone re-ligation steps. TrAC-loop selectively targets accessible regions, which effectively reduces the sequencing cost for detecting promoter-enhancer interactions at high resolution. Application of TrAC-loop to human CD4+ T cells reveals a substantial reorganization of enhancer-promoter interaction associated with changes in gene expression upon TCR stimulation.
Overall design Examination of enhancer-promoter interaction associated with changes in gene expression upon TCR stimulation.
Contributor(s) Lai B, Tang Q, Jin W, Hu G, Wangsa D, Cui K, Stanton BZ, Ren G, Ding Y, Zhao M, Song J, Ried T, Zhao K
Citation(s) 30150754
Submission date Sep 22, 2016
Last update date May 15, 2019
Contact name Keji Zhao
Organization name NHLBI,NIH
Department Systems Biology Center
Lab Laboratory of Epigenome Biology
Street address 9000 Rockville Pike
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (34)
GSM2326178 CD4_resting_rep1-tech1_TrAC-loop
GSM2326179 CD4_resting_rep2_TrAC-loop
GSM2326180 CD4_resting_rep1-rech2_TrAC-loop
BioProject PRJNA343953
SRA SRP090318

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

Supplementary file Size Download File type/resource
GSE87254_DHS1K_rest_2PETs_fdr.txt.gz 3.7 Mb (ftp)(http) TXT
GSE87254_DHS1K_rest_3PETs_fdr.txt.gz 2.3 Mb (ftp)(http) TXT
GSE87254_DHS1K_stim_2PETs_fdr.txt.gz 4.0 Mb (ftp)(http) TXT
GSE87254_DHS1K_stim_3PETs_fdr.txt.gz 2.4 Mb (ftp)(http) TXT
GSE87254_Human_CD4_stim_RPKM_Count_FDR_signifcant.xls.gz 626.8 Kb (ftp)(http) XLS
GSE87254_RAW.tar 8.8 Gb (http)(custom) TAR (of BEDGRAPH, BEDPE, TXT)
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Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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