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Sample GSM6998354 Query DataSets for GSM6998354
Status Public on Apr 21, 2023
Title TTseq_A375_cdk13_R860Q_rep2
Sample type SRA
Source name A375 melanoma cell line
Organism Homo sapiens
Characteristics tissue: A375 melanoma cell line
cell line: A375
genotype: pLENTI CMV CDK13 R860Q
Treatment protocol RNA was collected in Trizol per standard protocol.
Growth protocol Ribo-depleted RNA-seq and TT-seq were executed on equal numbers of human melanoma cells collected at the same time from pLENTI CMV CLOVER (n=3) and pLENTI CMV CDK13R860Q with spike in ERCC proportional to cell number (RNA-seq and TT-seq) (Thermofisher, 4456740) and 4sU labeled Drosophila S2 cell RNA (just TT-seq).
Extracted molecule total RNA
Extraction protocol TT-seq 4sU pulse was 5min and is otherwise as published (Schwalb et al., 2016).
NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (E7760S) was used for library prep and samples were sequenced with paired end sequencing on a HiSeq 2500
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
Description TT-seq
Data processing We aligned RNA-seq and TT-seq data to hg38 and to the transcriptome (genecode v26 ‘basic’ annotations) with STAR (Dobin et al., 2013). For data with spike-ins, we also aligned to the spike-in genomes, but as we observed no statistically significant difference in percent spike-in reads we depth normalized both the RNA-seq and TT-seq data.
Read coverage bigWig files were generated by STAR and then normalized by read depth.
Assembly: hg38
Supplementary files format and content: Read depth-normalized read coverage bigWig files
Submission date Jan 27, 2023
Last update date Apr 21, 2023
Contact name Richard A Young
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 GPL16791
Series (2)
GSE131334 Oncogenic CDK13 Mutations Impede Nuclear RNA Surveillance
GSE223888 Oncogenic CDK13 Mutations Impede Nuclear RNA Surveillance [humanTTseq]
BioSample SAMN32941377
SRA SRX19200037

Supplementary file Size Download File type/resource 103.4 Mb (ftp)(http) BW 103.0 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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