|
| Status |
Public on Jul 06, 2023 |
| Title |
CA-13_2 |
| Sample type |
SRA |
| |
|
| Source name |
paracancer tissue derived cells
|
| Organism |
Homo sapiens |
| Characteristics |
patient diagnosis: oral squamous cell carcinoma
cell type: paracancer tissue derived cells
genotype: WT
donor: donor 2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
CA1302
|
| Data processing |
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: md5
Supplementary files format and content: Differential_expression gene lists
|
| |
|
| Submission date |
Jan 13, 2023 |
| Last update date |
Jul 06, 2023 |
| Contact name |
Ming Guo Cao |
| E-mail(s) |
cmg@lsu.edu.cn
|
| Organization name |
Lishui University
|
| Street address |
No 01, Rd Xueyuan Avenue
|
| City |
Lishui |
| ZIP/Postal code |
323000 |
| Country |
China |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE222879 |
Glutamine synthetase regulates the alternative metabolism of γ-aminobutyrate in oral squamous cell carcinoma |
|
| Relations |
| BioSample |
SAMN32732114 |
| SRA |
SRX19031090 |
