|
| Status |
Public on Jan 20, 2020 |
| Title |
ND_3_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
mouse embryonic fibroblasts
|
| Organism |
Mus musculus |
| Characteristics |
cell type: mouse embryonic fibroblasts
cell line name: Mefs sg10
treatment: untreated
experimental series: PVT1 p53RE mutant doxorubicin timecourse
|
| Treatment protocol |
WT Mefs previously infected with an sgRNA targeting the PVT1 p53RE or a nontargeting control (sgtom) were untreated or grown in a 0.5uM concentration of doxorubicin for 24 hours to induce the DNA damage response.
|
| Growth protocol |
MEFs were grown in Dulbecco’s Modified Essential Media supplemented with 15% fetal bovine serum (Gibco), 0.1 mM nonessential amino acids, 2 mM L-glutamine, Pen/Strep (50 U/ml) and 0.055 mM β-mercaptoethanol.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted with Qiagen RNAeasy kit
Strand-specific RNA sequencing libraries from purified polyadenylated RNA were prepared using the TruSeq Stranded mRNA kit (Illumina)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
RNAseq library prepared with TruSeq stranded mRNA kit (illumina)
edgeR_sg10_sgtom_dox_gene_summary_180601.txt
|
| Data processing |
RNA-seq read files were merged from technical replicates.
Reads mapped to the mm10 genome assembly using Tophat (ver 2.0.14).
Additional transcripts were assembled using stringtie (1.2.4).
Reads within exon sequences counted using HTSeq (HTSeq-0.6.1).
Differential expression analysis was performed with EdgeR (3.22.3).
Genome_build: mm10
Supplementary_files_format_and_content: Processed data files contain normalized read counts for exonic regions and output from edgeR.
Supplementary_files_format_and_content: The data represents merged replicates
|
| |
|
| Submission date |
Feb 22, 2019 |
| Last update date |
Jan 20, 2020 |
| Contact name |
Jesse R Zamudio |
| E-mail(s) |
jesse.zamudio@ucla.edu
|
| Organization name |
University of California, Los Angeles
|
| Department |
MCDB
|
| Lab |
Zamudio
|
| Street address |
610 CHARLES E. YOUNG DRIVE EAST BOX 957239
|
| City |
LOS ANGELES |
| State/province |
CA |
| ZIP/Postal code |
90095-7239 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (2) |
| GSE126940 |
p53 activates the long noncoding RNA Pvt1b to inhibit Myc and suppress tumorigenesis |
| GSE143204 |
p53 activates the long noncoding RNA Pvt1b to inhibit Myc and suppress tumorigenesis |
|
| Relations |
| BioSample |
SAMN10988864 |
| SRA |
SRX5409976 |
