|
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 |