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Series GSE178377 Query DataSets for GSE178377
Status Public on Mar 31, 2022
Title Rhesus Macaque Model of Mismatch Repair-Deficient Colorectal Cancer (RRBS)
Organism Macaca mulatta
Experiment type Methylation profiling by high throughput sequencing
Summary Colorectal cancer (CRC) remains the third most common cancer in the US, with 15% of cases displaying Microsatellite Instability (MSI) secondary to Lynch Syndrome (LS) or somatic hypermethylation of the MLH1 promoter. A cohort of rhesus macaques from our institution developed spontaneous mismatch repair deficient (MMRd) CRC with a notable fraction harboring a pathogenic germline mutation in MLH1. DNA methylation and transcriptome analysis was performed to evaluate the rhesus macaque as a model organism to study carcinogenesis, develop immunotherapies and vaccines, and implement chemoprevention approaches pertinent to sporadic MSI-H and LS CRC in humans. 

NIH grant(s):

Grant ID: 5 P30 CA016672-44
Grant title: Cancer Center Support Grant
Affiliation: The University of Texas MD Anderson Cancer Center
Grantor: NCI

 
Overall design We performed reduced representation bisulfite sequencing (RRBS) in fourteen colorectal tumors and fourteen matched normal mucosa samples
 
Contributor(s) Vilar-Sanchez E, Deng N
Citation(s) 35446842
Submission date Jun 17, 2021
Last update date Jun 30, 2022
Contact name Eduardo Vilar-Sanchez
Organization name The University of Texas MD Anderson Cancer Center
Street address 1515 Holcombe Blvd
City Houston
State/province TX
ZIP/Postal code 77030
Country USA
 
Platforms (2)
GPL21326 Illumina MiSeq (Macaca mulatta)
GPL27943 Illumina NovaSeq 6000 (Macaca mulatta)
Samples (28)
GSM5389289 Tumor sample of Monkey RM33 (RRBS)
GSM5389290 Normal sample of Monkey RM33 (RRBS)
GSM5389291 Tumor sample of Monkey RM23 (RRBS)
This SubSeries is part of SuperSeries:
GSE178383 Rhesus Macaque Model of Mismatch Repair-Deficient Colorectal Cancer
Relations
BioProject PRJNA738802
SRA SRP324480

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE178377_RAW.tar 4.5 Gb (http)(custom) TAR (of BEDGRAPH)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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