|
| Status |
Public on Aug 15, 2024 |
| Title |
siBCAT1_1 |
| Sample type |
SRA |
| |
|
| Source name |
Lung adenocarcinoma
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Lung adenocarcinoma
cell line: ASK120067-resistant NCI-H1975 cells
cell type: NSCLC cells
genotype: BCAT1 knockdown
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from cells using TRIzol® Reagent according the manufacturer’s instructions.
The RNA-seq transcriptome librariy was prepared following Illumina® Stranded mRNA Prep, Ligation from Illumina (San Diego, CA) using 1μg of total RNA.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Illumina Casava1.7 software was used for basecalling
The raw paired end reads were trimmed and quality controlled by fastp with default parameters
Clean reads were separately aligned to reference genome with orientation mode using HISAT2 software
The mapped reads of each sample were assembled by StringTie in a reference-based approach
The expression level of each transcript was calculated according to the transcripts per million reads (TPM) method
Assembly: GRCh38,p13
Supplementary files format and content: tab-delimited text files include TPM values for each Sample
|
| |
|
| Submission date |
Nov 13, 2023 |
| Last update date |
Aug 15, 2024 |
| Contact name |
Zilu Pan |
| E-mail(s) |
[email protected]
|
| Organization name |
Shanghai Institute of Materia Medica
|
| Street address |
No. 555 Zuchongzhi Road
|
| City |
Shanghai |
| ZIP/Postal code |
201203 |
| Country |
China |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE247584 |
Molecular mechanisms of BCAT1 in ASK120067-resistant NSCLC cells |
|
| Relations |
| BioSample |
SAMN38228525 |
| SRA |
SRX22505017 |
