|
| Status |
Public on Jun 06, 2019 |
| Title |
CRC, primary, T42 |
| Sample type |
SRA |
| |
|
| Source name |
Colorectal cancer
|
| Organism |
Homo sapiens |
| Characteristics |
individual: patient P2
tissue: primary colorectal cancer (CRC) tissue
|
| Extracted molecule |
total RNA |
| Extraction protocol |
FFPE RNA was extracted using the Wuxi in-house method after FFPE sample sections were scalped into 1.5 mL microcentrifuge tubes, and then deparaffinization solution was used to remove paraffin. The RNA integrity was determined using a 2100 Bioanalyser (Agilent) with DV200 (Percentage of RNA fragments > 200 nt fragment distribution value) and quantified by the NanoDrop (Thermo Scientific).
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
RNA reads were generated, aligned to the GENCODE v19 genome assembly with STAR v2.4.1 and quantified using featureCounts v1.5.0.
The raw read counts were normalized with DESeq2 followed by differential expression analysis.
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited text files include normalized read counts for all samples
|
| |
|
| Submission date |
Jun 05, 2019 |
| Last update date |
Jun 06, 2019 |
| Contact name |
Cheng Wang |
| Organization name |
Nanjing Medicial University
|
| Street address |
No. 818 East Tianyuan Road
|
| City |
Nanjing |
| ZIP/Postal code |
211166 |
| Country |
China |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE132226 |
Genomic Signatures Reveal DNA Damage Response Deficiency in Brain Metastases of Colorectal Cancer |
|
| Relations |
| BioSample |
SAMN11961289 |
