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| Status |
Public on Jun 01, 2021 |
| Title |
Gene Expression Profiling of Mismatch Repair Deficient Intestinal Stem Cells |
| Organisms |
Homo sapiens; Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
We have generated a gene signature of mismatch repair (MMR) deficient intestinal stem cells (ISCs) using whole-genome transcriptomics and proteomics from murine intestinal stem cells and epithelial non-stem cells in a Lynch syndrome mouse model (Msh2-fl/fl;Villin-Cre). Then we have validated this signature in RNA-seq data from LS normal unaffected mucosa (UM), adenomas (AD) and adenomas with high-grade dsyplasia (AD-HGD) and tumors (T). MMR status for LS tumors and adenomas with high-grade dysplasia was categorized as KO, for unaffected mucosa as HET and FAP samples as WT.
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| Overall design |
We have performed mRNAseq using Illumina Hi-Seq in 3 mouse per genotype (9 total) and sequenced them in triplicated (total number of samples 18). 17 patients with FAP as controls (7 paired adenoma/mucosa samples and 10 unmatched normal mucosas) and 30 patients with LS (7 macthed tumor/adenomas with high-grade dysplasia and normal mucosa and 23 with normal mucosa only).
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| Contributor(s) |
Vilar E |
| Citation missing |
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| |
| Submission date |
Jun 26, 2020 |
| Last update date |
Aug 25, 2022 |
| Contact name |
Eduardo Vilar-Sanchez |
| E-mail(s) |
evilar@mdanderson.org
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| Phone |
713-563-4743
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| Organization name |
UT MD Anderson Cancer Center
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| Street address |
1515 Holcombe Blvd, Unit 1360
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| City |
Houston |
| State/province |
Texas |
| ZIP/Postal code |
77030-4000 |
| Country |
USA |
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| Platforms (3) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
| GPL20301 |
Illumina HiSeq 4000 (Homo sapiens) |
| GPL21103 |
Illumina HiSeq 4000 (Mus musculus) |
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| Samples (81)
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| Relations |
| SRA |
SRP268947 |
| BioProject |
PRJNA642180 |
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