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Sample GSM3618446 Query DataSets for GSM3618446
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

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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