|
| Status |
Public on Apr 15, 2014 |
| Title |
human colon, sample 33 |
| Sample type |
RNA |
| |
|
| Source name |
colon
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: colon
batch: 5
gender: M
in_eqtl: yes
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Maxwell 16 Tissue LEV Total RNA Purification Kit (Promega)
|
| Label |
biotin
|
| Label protocol |
Ambion MessageAmp kit for Illumina arrays
|
| |
|
| Hybridization protocol |
Standard Illumina hybridization protocol
|
| Scan protocol |
Standard Illumina scanning protocol
|
| Description |
Distal colonic biopsies from healthy African American subjects
|
| Data processing |
The Illumina GenomeStudio software was used to extract the signal intensities of each gene expression probe, which were then further preprocessed using the lumi package of Bioconductor in R. The preprocessing included background correction of the gene expression data, followed by variance-stabilizing transformation (VST), log2-transformation and quantile normalization. BLAT was used to map the probe sequences onto the RefSeq transcriptome. All probes mapping to multiple Entrez Gene IDs were excluded, and only probes with unique perfect matches to autosomal genes were kept. Probes that encompass a common SNP (MAF ≥ 5%) in either 1000 Genomes AFR or EUR populations were further excluded. Lastly, probes with an Illumina detection p-value < 0.01 in at least one individual were kept.
|
| |
|
| Submission date |
Apr 14, 2014 |
| Last update date |
Apr 15, 2014 |
| Contact name |
Sonia Kupfer |
| E-mail(s) |
[email protected]
|
| Phone |
773-702-8076
|
| Organization name |
University of Chicago
|
| Department |
Department of Medicine
|
| Street address |
900 East 57th Street, MB#9
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60637 |
| Country |
USA |
| |
|
| Platform ID |
GPL10558 |
| Series (1) |
| GSE56789 |
Enrichment of inflammatory bowel disease and colorectal cancer risk variants in colon expression quantitative trait loci |
|
