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Series GSE178341 Query DataSets for GSE178341
Status Public on Aug 26, 2021
Title A Single Cell Atlas of MMRd and MMRp Colorectal Cancer
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Immune responses to cancer are highly variable, in particular colorectal cancer tumors with mismatch repair-deficiency (MMRd) show an elevated presence and activity of immune cells as compared to mismatch repair proficient tumors. To understand the immune response patterns, and key differences between these types of colorectal cancer, we transcriptionally profiled 371,223 tumor and adjacent normal cells from 28 MMRp and 34 MMRd patients. Unsupervised analysis identified 88 cell subsets, from 7 distinct cell lineages, and an associated compendium of 204 gene expression programs. Examination of these programs revealed extensive transcriptional and spatial reprogramming, characteristic to MMRd and MMRp tumors.
 
Overall design A single cell expression study of primary treatment-naive colorectal cancer from MMR deficient, MMR proficient, and adjacent tumour samples.
***RNA-Seq raw data will be available through dbGaP (controlled access) due to patient privacy concerns: phs002407.v1.p1
Matan,Hofree
Web link https://portals.broadinstitute.org/crc-immune-hubs/
 
Contributor(s) Pelka K, Chen JH, Anderson AC, Rozenblatt-Rosen O, Regev A, Hachoen N
Citation(s) 34450029
Submission date Jun 16, 2021
Last update date Sep 02, 2021
Contact name Matan Hofree
E-mail(s) matan.hofree@mail.huji.ac.il
Organization name The Hebrew University of Jerusalem
Department School of Computer Science and Engineering | The Lautenberg Center for Immunology and Cancer Research
Lab Hofree lab
Street address The Edmond J. Safra, Givat Ram Campus
City Jerusalem
State/province NA
ZIP/Postal code 9190401
Country Israel
 
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (181)
GSM5387968 Single cell expression of human CRC samples from patient C103_T [C103_T_1_1_0_c1_v2]
GSM5387969 Single cell expression of human CRC samples from patient C103_T [C103_T_1_1_3_c1_v2]
GSM5387970 Single cell expression of human CRC samples from patient C104_T [C104_T_1_1_0_c1_v2]
Relations
BioProject PRJNA738517

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
GSE178341_crc10x_full_c295v4_submit.h5 1.1 Gb (ftp)(http) H5
GSE178341_crc10x_full_c295v4_submit_cluster.csv.gz 2.8 Mb (ftp)(http) CSV
GSE178341_crc10x_full_c295v4_submit_metatables.csv.gz 2.4 Mb (ftp)(http) CSV
Processed data are available on Series record
Raw data not provided for this record

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