|
| Status |
Public on Dec 09, 2019 |
| Title |
PB31-miR137 7 days ON # 2 |
| Sample type |
SRA |
| |
|
| Source name |
ßTC3 cells
|
| Organism |
Mus musculus |
| Characteristics |
cell line: betaTC3
plasmid: PB-31 miR-137
group: miR-137
treatment: 7 days DOX
replicate: 2
|
| 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 For the DOX OFF group, DOX was withdrawn after 7 days, and were cultured in regular DMEM media for another 7 days.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 |
SAMN11879346 |
| SRA |
SRX5914553 |
