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Sample GSM6012412 Query DataSets for GSM6012412
Status Public on Jul 12, 2023
Title primary CRC22.H
Sample type SRA
 
Source name primary colorectal cancer
Organism Homo sapiens
Characteristics tissue: colon
tissue type: non-neoplastic
Extracted molecule total RNA
Extraction protocol RNA was extracted from dissociated healthy, peritumoral and tumor samples using the ARCTURUS™ PicoPure™ RNA Isolation Kit (Thermofisher).
Libraries were prepared for sequencing using SMART-Seq v4 ultra-low RNA kit (Takara Bio)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing Reads were quality filtered according to the Illumina pipeline, then were aligned to mouse genome build GRCh38/hg38 using using START version 2.5.3a. Only uniquely mapped reads were retained.
Gene expression counts were estimated using featureCounts (version 1.6.4) , summarized across all exons , with option “largestOverlap”.
Differentially expressed genes were identified using EdgeR R-package (version 4.0.5).
Assembly: GRCh38/hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
 
Submission date Apr 04, 2022
Last update date Jul 12, 2023
Contact name Chiara Balestrieri
E-mail(s) balestrieri.c@gmail.com
Organization name IRCCS San Raffaele Scientific Institute
Department Center for Omics Sciences
Street address Via Olgettina 58
City Milan
ZIP/Postal code 20132
Country Italy
 
Platform ID GPL24676
Series (2)
GSE200130 Revealing and harnessing CD39 for the treatment of colorectal cancer and liver metastases by engineered T cells [CRC]
GSE200133 Revealing and harnessing CD39 for the treatment of colorectal cancer and liver metastases by engineered T cells
Relations
BioSample SAMN27290839
SRA SRX14729053

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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