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Series GSE66208 Query DataSets for GSE66208
Status Public on Jul 15, 2015
Title mRNA and small RNA associated with Crohn's disease behavior [ncRNA-Seq]
Organism Homo sapiens
Experiment type Non-coding RNA profiling by high throughput sequencing
Summary There is a need for reliable prognostic markers that can guide therapeutic intervention in Crohn’s disease (CD). We examined whether different behavioral phenotypes in CD can be classified based on colonic miRNA or mRNA expression and if miRNAs have prognostic utility for CD. We perform high-throughput sequencing of small RNA and mRNA isolated from colon tissue from CD patients and non-IBD (NIBD) controls. To identify miRNA and genes associated with specific behavioral phenotypes of CD, patients were stratified according to disease behavior (non-stricturing, non-penetrating; stricturing; penetrating) and compared miRNA profiles in each class with those of the NIBD group. Using a novel statistical simulation approach applied to colonic RNA-seq data for CD patients and NIBD controls, we identify at drivers of gene expression profiles associated with CD.
Overall design Macroscopically non-inflamed colon tissue from characterized Crohn's disease patients and normal controls were obtained. Small RNA-seq and RNA-seq were performed on these samples. Additionally, we investigated the effect of inflammation on miRNA expression by performing small RNA-seq on matched colon samples obtained from macroscopically inflamed regions from a subset (six) of these patients with CD.
Contributor(s) Sheikh SZ, Sethupathy P, Furey TS, Peck BC, Weiser M
Citation(s) 26164662
Submission date Feb 23, 2015
Last update date May 15, 2019
Contact name Bailey Peck
Organization name University of North Carolina at Chapel Hill
Department Genetics
Lab Sethupathy
Street address 120 Mason Farm Rd, 5100H Genetic Medicine Bldg
City Chapel Hill
State/province NC
ZIP/Postal code 27599
Country USA
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (41)
GSM1616945 Normal colon biopsy, female age 53 [ncRNA-Seq, 22_NIBD_NI]
GSM1616946 Normal colon acquired during Hartmann reversal after colon cancer, male age 52 [ncRNA-Seq, 23_NIBD_NI]
GSM1616947 Normal colon biopsy acquired during surgery for diverticulitis,female age 60 [ncRNA-Seq, 25_NIBD_NI]
This SubSeries is part of SuperSeries:
GSE66209 mRNA and small RNA associated with Crohn's disease behavior
BioProject PRJNA276115
SRA SRP055439

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Supplementary file Size Download File type/resource
GSE66208_Supplemental_Table_8_smRNAseq_ExpressionData.xlsx.gz 128.8 Kb (ftp)(http) XLSX
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Processed data are available on Series record
Raw data are available in SRA

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