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| Status |
Public on Apr 15, 2014 |
| Title |
Enrichment of inflammatory bowel disease and colorectal cancer risk variants in colon expression quantitative trait loci |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
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| Summary |
Genome wide association studies (GWAS) have identified single nucleotide polymorphisms (SNPs) associated with diseases of the colon including inflammatory bowel diseases (IBD) and colorectal cancer (CRC). However, the functional role of many of these SNPs is largely unknown and tissue-specific resources are lacking. Expression quantitative trait loci (eQTL) mapping identifies target genes of disease-associated SNPs. Here, we comprehensively map eQTLs in the human colon, assess their relevance for GWAS of colonic diseases and provide functional characterization.
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| Overall design |
Subjects included 40 healthy African American individuals who had undergone colonoscopy at the University of Illinois Chicago for screening purposes. Distal colonic biopsies were obtained in all subjects at 20 cm from the anal verge at the recto-sigmoid junction and were immediately dispensed in RNAlater. Total mRNA was extracted from manually ground tissue with the Promega Maxwell 16 Tissue LEV Total RNA Purification Kit for automated purification on the Maxwell 16 Instrument and mRNA analysis was performed on Illumina HumanHT-12v4 Expression BeadChip arrays. Genomic DNA was obtained from whole-blood samples from the same individuals and genotyped using the Affymetrix Axiom Genome-wide Pan-African array. Cis- and trans-eQTL analyses were performed on the dataset of 8.4 million imputed SNPs and 16,252 expression probes corresponding to 12,363 unique autosomal genes in 40 subjects. Associations between SNPs and gene expression levels were examined with Matrix eQTL using linear regression. False discovery rate calculations were performed separately for cis- and trans-eQTLs.
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| Contributor(s) |
Hulur I, Gamazon ER, Skol AD, Xicola R, Llor X, Onel K, Ellis NA, Kupfer S |
| Citation(s) |
25766683 |
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| Submission date |
Apr 14, 2014 |
| Last update date |
Aug 13, 2018 |
| Contact name |
Sonia Kupfer |
| E-mail(s) |
[email protected]
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| Phone |
773-702-8076
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| Organization name |
University of Chicago
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| Department |
Department of Medicine
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| Street address |
900 East 57th Street, MB#9
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| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60637 |
| Country |
USA |
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| Platforms (1) |
| GPL10558 |
Illumina HumanHT-12 V4.0 expression beadchip |
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| Samples (40)
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| GSM1369111 |
human colon, sample 4 |
| GSM1369112 |
human colon, sample 5 |
| GSM1369113 |
human colon, sample 6 |
| GSM1369114 |
human colon, sample 7 |
| GSM1369115 |
human colon, sample 8 |
| GSM1369116 |
human colon, sample 9 |
| GSM1369117 |
human colon, sample 10 |
| GSM1369118 |
human colon, sample 11 |
| GSM1369119 |
human colon, sample 12 |
| GSM1369120 |
human colon, sample 13 |
| GSM1369121 |
human colon, sample 14 |
| GSM1369122 |
human colon, sample 15 |
| GSM1369123 |
human colon, sample 18 |
| GSM1369124 |
human colon, sample 19 |
| GSM1369125 |
human colon, sample 20 |
| GSM1369126 |
human colon, sample 21 |
| GSM1369127 |
human colon, sample 22 |
| GSM1369128 |
human colon, sample 23 |
| GSM1369129 |
human colon, sample 24 |
| GSM1369130 |
human colon, sample 25 |
| GSM1369131 |
human colon, sample 26 |
| GSM1369132 |
human colon, sample 27 |
| GSM1369133 |
human colon, sample 28 |
| GSM1369134 |
human colon, sample 32 |
| GSM1369135 |
human colon, sample 33 |
| GSM1369136 |
human colon, sample 36 |
| GSM1369137 |
human colon, sample 37 |
| GSM1369138 |
human colon, sample 38 |
| GSM1369139 |
human colon, sample 39 |
| GSM1369140 |
human colon, sample 40 |
| GSM1369141 |
human colon, sample 41 |
| GSM1369142 |
human colon, sample 42 |
| GSM1369143 |
human colon, sample 43 |
| GSM1369144 |
human colon, sample 44 |
| GSM1369145 |
human colon, sample 46 |
| GSM1369146 |
human colon, sample 47 |
| GSM1369147 |
human colon, sample 48 |
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| Relations |
| BioProject |
PRJNA244588 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE56789_Non-normalized_data.txt.gz |
13.6 Mb |
(ftp)(http) |
TXT |
| GSE56789_RAW.tar |
26.2 Mb |
(http)(custom) |
TAR |
| Processed data included within Sample table |
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