|
Status |
Public on Apr 21, 2023 |
Title |
RNAseq_siZFC3H1_1_A375 |
Sample type |
SRA |
|
|
Source name |
melanoma cell line
|
Organism |
Homo sapiens |
Characteristics |
tissue: melanoma cell line genotype: siZFC3H1 cell line: A375
|
Treatment protocol |
Stable lines were untreated. Knockdown of ZFC3H1 (Dharmacon, L-020839-02-0005), ZC3H14 (Dharmacon, L-014468-01-0005), or a control knockdown (Dharmacon, D-001810-01-05) were completed on A375 CLOVER cells
|
Growth protocol |
A375 human melanoma cells were identity-verified via STR analysis. Mycoplasma testing was done within one week of every experiment using human cell lines (Lonza, Mycoalert PLUS, LT07-710). All cell lines were mycoplasma negative. Cells were grown in DMEM supplemented with 10% FBS, penicillin/streptomycin or selection antibiotics, and L-glutamine.
|
Extracted molecule |
polyA RNA |
Extraction protocol |
DNA was removed, and RNA was isolated (Qiagen, 741134). Poly-A selection was undertaken (NEB, E7490). NEBNext® Ultra™ Directional RNA Library Prep Kit
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2000 |
|
|
Data processing |
Mapped using STAR aligner version 2.7.2a (Dobin et al., 2013). Using splice junctions and the mapped 3' cleavage and adenylation sites from the 3'seq data, custom transcriptomic annotations were produced with our custom alpha3pseq pipeline software. This produced a gtf file with intronic and alternative polyadenylation sites. The annotation from alpha3pseq was used to count mapped reads above using the DEXseq/Htseq counting scripts. This produced the read counts tables in this dataset. Assembly: GRCh38 Supplementary files format and content: Count tables
|
|
|
Submission date |
Jan 27, 2023 |
Last update date |
Apr 21, 2023 |
Contact name |
Richard A Young |
E-mail(s) |
young_computation@wi.mit.edu
|
Phone |
617-258-5219
|
Organization name |
Whitehead Institute for Biomedical Research
|
Lab |
Young Lab
|
Street address |
9 Cambridge Center
|
City |
Cambridge |
State/province |
MA |
ZIP/Postal code |
02142 |
Country |
USA |
|
|
Platform ID |
GPL11154 |
Series (2) |
GSE131334 |
Oncogenic CDK13 Mutations Impede Nuclear RNA Surveillance |
GSE223891 |
Oncogenic CDK13 Mutations Impede Nuclear RNA Surveillance [humanpolyARNAseq] |
|
Relations |
BioSample |
SAMN32941431 |
SRA |
SRX19200312 |