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Series GSE86189 Query DataSets for GSE86189
Status Public on Jul 31, 2019
Title A compendium of promoter-centered long-range chromatin interactions in diverse human tissues and cell types
Organism Homo sapiens
Experiment type Other
Summary A large number of genetic variants associated with human diseases are found in non-coding DNA and may contribute to illness by affecting gene regulation, but mechanistic study of these variants has been hindered by a lack of information of their potential regulatory targets. In order to overcome this limitation, we generate maps of long-range chromatin interactions centered on 19,539 promoters in 27 human cell/tissue types, and use this information to infer putative target genes of candidate cis-regulatory sequences throughout the human genome. In additional to known enhancer-promoter interactions, we also confirm widespread promoter-promoter interactions and obtain evidence suggesting enhancer-like function for many promoter regions. These promoter-centered chromatin interaction maps corroborate target genes of genetic variants defined in previous genome-wide association studies, predict new target genes of many disease-associated genetic variants, and contribute novel insights into a broad spectrum of human traits and diseases.
 
Overall design The study contains promoter capture Hi-C results for diverse human cell/tissue types
.bz2, text files for promoter capture Hi-C chromatin interaction between DNA fragments for promoter-promoter interactions (PP) or promoter-other interactions (PO)
pp: P-P interaction frequency
po: P-O interaction frequency
Web link http://www.3div.kr/capture_hic
 
Contributor(s) Jung I, Schmitt A, Lee A, Ren B
Citation(s) 31501517
Submission date Aug 29, 2016
Last update date Dec 05, 2019
Contact name Inkyung Jung
E-mail(s) ijungkaist@gmail.com
Organization name KAIST
Department Biological Sciences
Street address KAIST, 291 Daehak-ro, Yuseong-gu
City Daejeon
ZIP/Postal code 34141
Country South Korea
 
Platforms (3)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
GPL20301 Illumina HiSeq 4000 (Homo sapiens)
Samples (249)
GSM2297098 STL002.AD2.ADS166
GSM2297099 STL002.AD2.ADS256
GSM2297100 STL002.AD2.ADS268
Relations
BioProject PRJNA340778
SRA SRP083285

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
GSE86189_AD.po.all.txt.gz 156.4 Mb (ftp)(http) TXT
GSE86189_AD.pp.all.txt.gz 8.4 Mb (ftp)(http) TXT
GSE86189_AO.po.all.txt.gz 156.5 Mb (ftp)(http) TXT
GSE86189_AO.pp.all.txt.gz 8.4 Mb (ftp)(http) TXT
GSE86189_BL.po.all.txt.gz 156.5 Mb (ftp)(http) TXT
GSE86189_BL.pp.all.txt.gz 8.4 Mb (ftp)(http) TXT
GSE86189_CM.po.all.txt.gz 157.0 Mb (ftp)(http) TXT
GSE86189_CM.pp.all.txt.gz 8.5 Mb (ftp)(http) TXT
GSE86189_DLPFC.po.all.txt.bz2 94.8 Mb (ftp)(http) TXT
GSE86189_DLPFC.pp.all.txt.bz2 6.0 Mb (ftp)(http) TXT
GSE86189_EG.po.all.txt.bz2 92.7 Mb (ftp)(http) TXT
GSE86189_EG.pp.all.txt.bz2 5.9 Mb (ftp)(http) TXT
GSE86189_FT.po.all.txt.bz2 92.9 Mb (ftp)(http) TXT
GSE86189_FT.pp.all.txt.bz2 5.9 Mb (ftp)(http) TXT
GSE86189_GA.po.all.txt.bz2 94.8 Mb (ftp)(http) TXT
GSE86189_GA.pp.all.txt.bz2 6.0 Mb (ftp)(http) TXT
GSE86189_GM.po.all.txt.bz2 98.0 Mb (ftp)(http) TXT
GSE86189_GM.pp.all.txt.bz2 6.3 Mb (ftp)(http) TXT
GSE86189_H1.po.all.txt.bz2 95.8 Mb (ftp)(http) TXT
GSE86189_H1.pp.all.txt.bz2 6.1 Mb (ftp)(http) TXT
GSE86189_HC.po.all.txt.bz2 95.1 Mb (ftp)(http) TXT
GSE86189_HC.pp.all.txt.bz2 6.1 Mb (ftp)(http) TXT
GSE86189_LG.po.all.txt.bz2 94.9 Mb (ftp)(http) TXT
GSE86189_LG.pp.all.txt.bz2 6.0 Mb (ftp)(http) TXT
GSE86189_LI.po.all.txt.bz2 94.8 Mb (ftp)(http) TXT
GSE86189_LI.pp.all.txt.bz2 6.0 Mb (ftp)(http) TXT
GSE86189_LV.po.all.txt.bz2 95.5 Mb (ftp)(http) TXT
GSE86189_LV.pp.all.txt.bz2 6.1 Mb (ftp)(http) TXT
GSE86189_ME.po.all.txt.bz2 95.7 Mb (ftp)(http) TXT
GSE86189_ME.pp.all.txt.bz2 6.1 Mb (ftp)(http) TXT
GSE86189_OV.po.all.txt.bz2 93.9 Mb (ftp)(http) TXT
GSE86189_OV.pp.all.txt.bz2 6.0 Mb (ftp)(http) TXT
GSE86189_PA.po.all.txt.bz2 94.4 Mb (ftp)(http) TXT
GSE86189_PA.pp.all.txt.bz2 6.0 Mb (ftp)(http) TXT
GSE86189_PO.po.all.txt.bz2 93.5 Mb (ftp)(http) TXT
GSE86189_PO.pp.all.txt.bz2 5.9 Mb (ftp)(http) TXT
GSE86189_RA.po.all.txt.bz2 92.7 Mb (ftp)(http) TXT
GSE86189_RA.pp.all.txt.bz2 5.9 Mb (ftp)(http) TXT
GSE86189_RAW.tar 15.1 Mb (http)(custom) TAR (of BEDPE, FPKM_TRACKING)
GSE86189_RV.po.all.txt.bz2 95.2 Mb (ftp)(http) TXT
GSE86189_RV.pp.all.txt.bz2 6.1 Mb (ftp)(http) TXT
GSE86189_SB.po.all.txt.bz2 94.8 Mb (ftp)(http) TXT
GSE86189_SB.pp.all.txt.bz2 6.0 Mb (ftp)(http) TXT
GSE86189_SG.po.all.txt.bz2 92.6 Mb (ftp)(http) TXT
GSE86189_SG.pp.all.txt.bz2 5.9 Mb (ftp)(http) TXT
GSE86189_SX.po.all.txt.bz2 94.3 Mb (ftp)(http) TXT
GSE86189_SX.pp.all.txt.bz2 6.0 Mb (ftp)(http) TXT
GSE86189_TB.po.all.txt.bz2 94.6 Mb (ftp)(http) TXT
GSE86189_TB.pp.all.txt.bz2 6.0 Mb (ftp)(http) TXT
GSE86189_TH.po.all.txt.bz2 95.0 Mb (ftp)(http) TXT
GSE86189_TH.pp.all.txt.bz2 6.1 Mb (ftp)(http) TXT
GSE86189_all_interaction.po.txt.gz 22.9 Mb (ftp)(http) TXT
GSE86189_all_interaction.pp.txt.gz 2.2 Mb (ftp)(http) TXT
GSE86189_imr90.po.all.txt.bz2 95.8 Mb (ftp)(http) TXT
GSE86189_imr90.pp.all.txt.bz2 6.1 Mb (ftp)(http) TXT
GSE86189_msc.po.all.txt.bz2 96.8 Mb (ftp)(http) TXT
GSE86189_msc.pp.all.txt.bz2 6.2 Mb (ftp)(http) TXT
GSE86189_npc.po.all.txt.bz2 94.1 Mb (ftp)(http) TXT
GSE86189_npc.pp.all.txt.bz2 6.0 Mb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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