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Sample GSM6998384 Query DataSets for GSM6998384
Status Public on Apr 21, 2023
Title RNAseq_siCtrl_2_A375
Sample type SRA
 
Source name melanoma cell line
Organism Homo sapiens
Characteristics tissue: melanoma cell line
genotype: siControl
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 SAMN32941436
SRA SRX19200307

Supplementary file Size Download File type/resource
GSM6998384_Human_RNAseq_DEXSeq_Raw_Counts_siCtrl_R2.txt.gz 2.5 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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