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| Status |
Public on Jul 15, 2015 |
| Title |
mRNA and small RNA associated with Crohn's disease behavior [RNA-Seq] |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| 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.
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| Overall design |
Macroscopically non-inflamed colon tissue from well-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 Crohn's Disease.
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| 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 |
| E-mail(s) |
bpeck@email.unc.edu
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| Organization name |
University of North Carolina at Chapel Hill
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| Department |
Genetics
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| Lab |
Sethupathy
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| Street address |
120 Mason Farm Rd, 5100H Genetic Medicine Bldg
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| City |
Chapel Hill |
| State/province |
NC |
| ZIP/Postal code |
27599 |
| Country |
USA |
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| Platforms (1) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
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| Samples (33)
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| GSM1616912 |
B2/stricturing Crohn's disease [RNA-Seq, 20_CD_NI_B2] |
| GSM1616913 |
B2/stricturing Crohn's disease [RNA-Seq, 21_CD_NI_B2] |
| GSM1616914 |
B3/penetrating Crohn's disease [RNA-Seq, 29_CD_NI_B3] |
| GSM1616915 |
B2/stricturing Crohn's disease [RNA-Seq, 51_CD_NI_B2] |
| GSM1616916 |
B1/non-strituring, non-penetrating Crohn's disease [RNA-Seq, 54_CD_NI_B1] |
| GSM1616917 |
B3/penetrating Crohn's disease [RNA-Seq, 62_CD_NI_B3] |
| GSM1616918 |
B1/non-strituring, non-penetrating Crohn's disease [RNA-Seq, 63_CD_NI_B1] |
| GSM1616919 |
B3/penetrating Crohn's disease [RNA-Seq, 64_CD_NI_B3] |
| GSM1616920 |
B1/non-strituring, non-penetrating Crohn's disease [RNA-Seq, 405_CD_NI_B1] |
| GSM1616921 |
B3/penetrating Crohn's disease [RNA-Seq, 407_CD_NI_B3] |
| GSM1616922 |
B1/non-strituring, non-penetrating Crohn's disease [RNA-Seq, 408_CD_NI_B1] |
| GSM1616923 |
B3/penetrating Crohn's disease [RNA-Seq, 413_CD_NI_B1] |
| GSM1616924 |
B2/stricturing Crohn's disease [RNA-Seq, 420_CD_NI_B2] |
| GSM1616925 |
B2/stricturing Crohn's disease [RNA-Seq, 422_CD_NI_B2] |
| GSM1616926 |
B3/penetrating Crohn's disease [RNA-Seq, 424_CD_NI_B3] |
| GSM1616927 |
B1/non-strituring, non-penetrating Crohn's disease [RNA-Seq, 429_CD_NI_B1] |
| GSM1616928 |
B1/non-strituring, non-penetrating Crohn's disease [RNA-Seq, 431_CD_NI_B1] |
| GSM1616929 |
B3/penetrating Crohn's disease [RNA-Seq, 434_CD_NI_B3] |
| GSM1616930 |
B2/stricturing Crohn's disease [RNA-Seq, 440_CD_NI_B2] |
| GSM1616931 |
B3/penetrating Crohn's disease [RNA-Seq, 450_CD_NI_B3] |
| GSM1616932 |
Normal colon biopsy, female age 53 [RNA-Seq, 22_NIBD_NI] |
| GSM1616933 |
Normal colon acquired during Hartmann reversal after colon cancer, male age 52 [RNA-Seq, 23_NIBD_NI] |
| GSM1616934 |
Normal colon biopsy acquired during surgery for diverticulitis,female age 60 [RNA-Seq, 25_NIBD_NI] |
| GSM1616935 |
Normal colon acquired during surgery for diverticulitis, male age 70 [RNA-Seq, 27_NIBD_NI] |
| GSM1616936 |
Normal colon biopsy acquired during surgery for colon cancer, female age 82 [RNA-Seq, 30_NIBD_NI] |
| GSM1616937 |
Normal colon acquired during surgery for colon cancer, male age 44 [RNA-Seq, 32_NIBD_NI] |
| GSM1616938 |
Normal colon acquired during surgery for colonic inertia, female age 41 [RNA-Seq, 36_NIBD_NI] |
| GSM1616939 |
Normal colon acquired during surgery for colon cancer, male age 52 [RNA-Seq, 39_NIBD_NI] |
| GSM1616940 |
Normal colon acquired during surgery for large polyp, male age 65 [RNA-Seq, 42_NIBD_NI] |
| GSM1616941 |
Normal colon acquired during surgery for colonic inertia, female age 45 [RNA-Seq, 43_NIBD_NI] |
| GSM1616942 |
Normal colon acquired during surgery for adenoma, male age 70 [RNA-Seq, 48_NIBD_NI] |
| GSM1616943 |
Normal colon acquired during surgery for adenoma, male age 62 [RNA-Seq, 49_NIBD_NI] |
| GSM1616944 |
Normal colon acquired during surgery for small intestine neuroendocrine tumor, female age 49 [RNA-Seq, 50_NIBD_NI] |
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| This SubSeries is part of SuperSeries: |
| GSE66209 |
mRNA and small RNA associated with Crohn's disease behavior |
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| Relations |
| BioProject |
PRJNA276116 |
| SRA |
SRP055438 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE66207_Normalized_AllCD_AllControl_GEO.txt.gz |
2.4 Mb |
(ftp)(http) |
TXT |
| GSE66207_ReadCounts_AllCD_AllControl_GEO.txt.gz |
1.1 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Processed data are available on Series record |
| Raw data are available in SRA |
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