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Sample GSM3824005 Query DataSets for GSM3824005
Status Public on Dec 09, 2019
Title PB31-miR137 no dox # 3
Sample type SRA
 
Source name ßTC3 cells
Organism Mus musculus
Characteristics cell line: betaTC3
plasmid: PB-31 miR-137
group: miR-137
treatment: no DOX
replicate: 3
Treatment protocol For the 7 days DOX group, cells were cultured in DMEM media containing DOX (2µg/ml) for 7 days. For the DOX OFF group, DOX was withdrawn after 7 days, and were cultured in regular DMEM media for another 7 days. No DOX groups were cultured for 7 days in regular DMEM media.
Growth protocol ßTC3 cells were plated in 6-well plates in triplicate.
Extracted molecule polyA RNA
Extraction protocol Cells were isolated and RNA was harvested using Trizol reagent. TruSeq stranded mRNA kit (Illumina) was used to prepare sequencing libraries, starting from 500ng total RNA.
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Data processing Illumina Real Time Analysis software (RTA) 1.18.61 software was used for base calling
Purity-filtered reads were adapters and quality trimmed with Cutadapt (v. 1.3, Martin 2011) and filtered for low complexity with seq_crumbs (v. 0.1.8).
Reads were aligned against Mus musculus.GRCm38.82 genome using STAR (v. 2.4.0g, Dobin et al. 2013).
The number of read counts per gene locus was summarized with htseq-count (v. 0.6.1, Anders et al. 2014) using Mus musculus.GRCm38.82 gene annotation.
Quality of the RNA-seq data alignment was assessed using RSeQC (v. 2.3.7, Wang et al. 2012)
Reads were also aligned to the Mus musculus.GRCm38.82 transcriptome using STAR (v. 2.4.0g, Dobin et al. 2013) and the estimation of the isoforms abundance was computed using RSEM (v. 1.2.19, Li and Dewey 2011).
Genome_build: mm10
Supplementary_files_format_and_content: tab separated raw counts from featureCounts with Ensembl gene ID, tab separated RSEM normalized TPM with Ensembl gene ID
 
Submission date May 29, 2019
Last update date Dec 10, 2019
Contact name Nadine Fournier
E-mail(s) [email protected]
Organization name Agora Cancer Research Center & Swiss Institute of Bioinformatics
Lab Translational Data Science Facility
Street address Agora Cancer Research Center, Bugon 25A
City Lausanne
State/province Vaud
ZIP/Postal code 1000
Country Switzerland
 
Platform ID GPL17021
Series (1)
GSE131887 Analysis of gene expression from ßTC3 cells of Rip-Tag2 PanNET mouse model upon miR-137 and miR-23b cluster doxycycline (DOX) induction
Relations
BioSample SAMN11879348
SRA SRX5914551

Supplementary file Size Download File type/resource
GSM3824005_434.gene_counts.txt.gz 165.8 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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