GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE69600 Query DataSets for GSE69600
Status Public on Nov 24, 2015
Title Capture Hi-C reveals novel candidate genes and complex long-range interactions with related autoimmune risk loci
Organism Homo sapiens
Experiment type Other
Summary Genome-wide association studies have been tremendously successful in identifying genetic variants associated with complex diseases. The majority of association signals are intergenic and evidence is accumulating that a high proportion of signals lie in enhancer regions.We use Capture Hi-C to investigate, for the first time, the interactions between associated variants for four autoimmune diseases and their functional targets in B- and T-cell lines. Here we report numerous looping interactions and provide evidence that only a minority of interactions are common to both B- and T-cell lines, suggesting interactions may be highly cell-type specific; some disease-associated SNPs do not interact with the nearest gene but with more compelling candidate genes (for example, FOXO1, AZI2) often situated several megabases away; and finally, regions associated with different autoimmune diseases interact with each other and the same promoter suggesting common autoimmune gene targets (for example, PTPRC, DEXI and ZFP36L1).
Overall design Capture Hi-C was carried out to characterise the interactions of confirmed susceptibility loci for four autoimmune diseases: rheumatoid arthritis (RA), type 1 diabetes (T1D), psoriatic arthritis (PsA) and juvenile idiopathic arthritis (JIA) with the aim of linking associated variants with disease-causing genes. We have tested the interactions in two complementary experiments: the first, Region Capture, targets regions associated with disease; the second, Promoter Capture, provides independent validation through capturing all known promoters within 500kb of lead associated disease SNPs. All experiments were performed in human T-cell (Jurkat) and B-cell (GM12878) lines in duplicate.
Contributor(s) Martin P, McGovern A, Orozco G, Duffus K, Yarwood A, Barton A, Worthington J, Eyre S
Citation(s) 26616563, 27861577
Submission date Jun 05, 2015
Last update date May 15, 2019
Contact name Paul Martin
Organization name Univeristy of Manchester
Department Centre for Genetics and Genomics Versus Arthritis
Street address Oxford Road
City Manchester
State/province Greater Manchester
ZIP/Postal code M13 9PT
Country United Kingdom
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (4)
GSM1704493 Region Capture Hi-C, GM12878 Lymphoblastoid cells, replicate one & two
GSM1704494 Region Capture Hi-C, Jurkat T lymphocyte cells, replicate one & two
GSM1704495 Promoter Capture Hi-C, GM12878 Lymphoblastoid cells, replicate one & two
BioProject PRJNA285958
SRA SRP059186

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
GSE69600_RAW.tar 1.9 Gb (http)(custom) TAR (of BEDPE)
GSE69600_promoter_capture_bait_coordinates.bed.gz 65.1 Kb (ftp)(http) BED
GSE69600_region_capture_bait_coordinates.bed.gz 24.1 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap