|
| Status |
Public on Jan 16, 2024 |
| Title |
L1EHB2200220--siACSL5_2260_3, ACSL5 KO |
| Sample type |
SRA |
| |
|
| Source name |
KPC1199
|
| Organism |
Mus musculus |
| Characteristics |
cell line: KPC1199
cell type: Pancreatic tumor cells
genotype: ACSL5 knockdown
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from the tissue using TRIzol® Reagent according the manufacturer’s instructions. Then RNA quality was determined by 5300 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies).
RNA purification, reverse transcription, library construction and sequencing were performed at Shanghai Majorbio Bio-pharm Biotechnology Co., Ltd. (Shanghai, China) according to the manufacturer’s instructions (Illumina, San Diego, CA)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
siACSL5_2260_3
|
| Data processing |
The raw paired end reads were trimmed and quality controlled by fastp with default parameters.
Then clean reads were separately aligned to hg38 with orientation mode using HISAT2 software
The mapped reads of each sample were assembled by StringTie in a reference-based approach
differential expression analysis was performed using the DESeq2
Assembly: GRCh38
Supplementary files format and content: Tab-delimited sheet includes tpm of each sample
Supplementary files format and content: Tab-delimited sheet includes count of each sample
|
| |
|
| Submission date |
Jan 16, 2024 |
| Last update date |
Jan 16, 2024 |
| Contact name |
jun yi Xu |
| E-mail(s) |
xujunyi0509@sjtu.edu.cn
|
| Organization name |
Shanghaijiaotong university
|
| Street address |
160 Pujian Rd
|
| City |
Shanghai |
| State/province |
Shanghai |
| ZIP/Postal code |
200120 |
| Country |
China |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE253315 |
Deciphering Fatty Acid Biosynthesis-Driven Molecular Subtypes in Pancreatic Ductal Adenocarcinoma with Prognostic Insights |
|
| Relations |
| BioSample |
SAMN39456877 |
| SRA |
SRX23228357 |
