|
Status |
Public on Apr 21, 2023 |
Title |
TTseq_A375_Ctrl_rep3 |
Sample type |
SRA |
|
|
Source name |
A375 melanoma cell line
|
Organism |
Homo sapiens |
Characteristics |
tissue: A375 melanoma cell line cell line: A375 genotype: pLENTI CMV CLOVER
|
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 |
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 |
GPL16791 |
Series (2) |
GSE131334 |
Oncogenic CDK13 Mutations Impede Nuclear RNA Surveillance |
GSE223888 |
Oncogenic CDK13 Mutations Impede Nuclear RNA Surveillance [humanTTseq] |
|
Relations |
BioSample |
SAMN32941379 |
SRA |
SRX19200035 |