|
| Status |
Public on Nov 07, 2023 |
| Title |
A375 cells, shPRMT1_1,rep3 |
| Sample type |
SRA |
| |
|
| Source name |
cell line
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: cell line
cell line: A375
cell type: melanoma cells
genotype: PRMT1 knockdown
|
| Growth protocol |
B16-F10 and A375 cells were maintained in DMEM medium containing 1% Penicillin/Streptomycin and 10% FBS andcultured in 37°C incubator with 5%CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The total RNA from B16-F10 or A375 cells was extracted by trizol(Vazyme) according to manufacturer’s protocol for RNA-seq. For chip-seq, B16-F10 cells were fixed by 1% formaldehyde for 10 minutes. Then, chromatin from cells lysate was digested by Micrococcal Nuclease into DNA fragments between 150-900 bp in length and released by sonication for antibody enrichment.
RNA libraries for RNA-seq were prepared using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina(Vazyme) following manfacturer's protocl.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
A375_shNC_shPRMT1.txt
|
| Data processing |
FastQC was used to qualified the reads.
The qualified reads were mapped on homo sapiens genome hg38 by STAR(2.7.10b).
The gene counts were quantified by featureCounts (subread 2.0.1).
Gtf files were generated using stringtie.
Gtf files were imported into ASprofile to compare multiple transcripts of the same gene for identification of variable indirect events
Assembly: hg38
|
| |
|
| Submission date |
Aug 07, 2023 |
| Last update date |
Nov 07, 2023 |
| Contact name |
Liyuan Zhou |
| E-mail(s) |
zhouliyaun21@mails.ucas.ac.cn
|
| Organization name |
University of Chinese Academy of Sciences
|
| Street address |
国科大杭州高等研究院
|
| City |
Hangzhou |
| State/province |
杭州市 |
| ZIP/Postal code |
310024 |
| Country |
China |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE240258 |
PRMT1 inhibition activates the interferon pathway to potentiate antitumor immunity and enhance checkpoint blockade efficacy in melanoma |
|
| Relations |
| BioSample |
SAMN36873423 |
| SRA |
SRX21282169 |
