Dataset features

Specifications


Application: Gene expression microarray analysis
Number of samples: 57
Release date: Nov 1 2018
Last update date: Nov 2 2018
Access: Public
Diseases: Colitis, Ulcerative, Colonic Diseases, Crohn Disease, Inflammatory Bowel Diseases
Chemicals: Azathioprine
Genes: TPMT, SLC26A3, DUOX2, DUOXA2
Taxon: Homo sapiens
Dataset link Elevation in cell cycle and protein metabolism gene transcription in inactive colonic tissue from Icelandic patients with ulcerative colitis

Experimental Protocol


The original expression data contained 47,198 probes and 57 samples: 27 ascending colon and 30 rectal taken from the 35 individuals. For ascending colon samples, there were 12 cases and 15 controls, and for rectal samples, 15 cases and 15 controls. Probes with a minimum detection P-value of < 0.01 in at least 2 biopsies were retained (n = 22,716). Two case samples (1 ascending colon HCA12, 1 rectal HCR10) with significantly lower numbers of detected probes were excluded. Retained probes were mapped to gene IDs by the illuminaHumanv4.db package. Adjustment of the expression data for chip-level batch effects was done by the empirical Bayes method ComBat24 (sva R package25). The recorded bowel sites were verified by examining expression of genes known to significantly differ between the ascending colon and rectum and through a PCA on all probes: 1 ascending colon (UCA20) and 2 rectal samples (UCR11, UCR18) demonstrated discordant expression from expected and were removed. Post-QC, there were 52 samples (24 cases, 28 controls), of which 25 were ascending colon (11 cases, 14 controls), and 27 were rectal (13 cases, 14 controls). These data were log2 transformed, quantile normalised and analysed in R using various Bioconductor packages.

Repositories


GEO

GSE105074

BioProject

PRJNA414600

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Contact


Tony Segal