|
| Status |
Public on Aug 14, 2019 |
| Title |
32-CD8 RNA seq |
| Sample type |
SRA |
| |
|
| Source name |
hepatocellular carcinoma tissue
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: CD8 T cells
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Cells were cryopreserved in Trizol reagent and RNA extracted according to the manufacturer’s instructions.
Total RNA quality was assessed with the Agilent 2100 Bioanalyzer System. Extracted RNA samples were processed using the QuantSeq 3’ mRNA-Seq Library Prep Kit (Lexogen, Vienna) and sequenced on an Illumina NextSeq 500. A median 2.0x107 (range 1.7x107 to 2.4x107) single-end reads with 75 bp were generated.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
32-CD8
|
| Data processing |
Reads were trimmed based on sequencing quality using Sickle.
Poly-A tails and adaptor contents were removed using Cutadapt.
Trimmed reads were aligned on a human reference sequence (hg19) using Tophat2.
The number of mapped reads on the 3’ end of each gene was calculated using Bedtools.
Genome_build: hg19
Supplementary_files_format_and_content: Raw read count
|
| |
|
| Submission date |
Jun 17, 2019 |
| Last update date |
Aug 14, 2019 |
| Contact name |
Su-Hyung Park |
| E-mail(s) |
park3@kaist.ac.kr
|
| Organization name |
Korea Advanced Institute of Science and Technology
|
| Street address |
291 Daehak-ro
|
| City |
Daejeon |
| ZIP/Postal code |
34141 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE132812 |
Gene expression profiles of tumor-infiltrating CD8 T cells in hepatocellular carcinoma |
|
| Relations |
| BioSample |
SAMN12071908 |
| SRA |
SRX6076610 |
