|
| Status |
Public on Feb 04, 2020 |
| Title |
Beko_DMSO_(GSI_ Ctrl)_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Beko_DMSO_(GSI_ Ctrl)
|
| Organism |
Mus musculus |
| Characteristics |
cell type: pre-T cells (Beko)
treated with: DMSO for 24hrs
molecule subtype: RiboMinus - depleted total RNA
|
| Treatment protocol |
Mouse pre-T (Beko) cells were treated for 24 hours with 0.01 µg/ml apicidin, 10 µg/ml DAPT (GSI) or with DMSO as control. Alternatively, Beko cells were infected with plasmids driving the expression of shRNAs against Hdac3 or scrambled (SCR) as control.
|
| Growth protocol |
Mouse pre-T (Beko) cells were grown at 37°C with 5% CO2 in IMDM medium (Gibco 21980-065) supplemented with 2% FCS, peptone, insulin, nonessential aminoacids and penicillin/streptomycin.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Rneasy Mini Kit (Qiagen #74104) using the QIAshredder (Qiagen #79654) and RNase-free DNase (Qiagen #79254).
Lybrary-prep kit: Illumina TruSeq® Stranded Total RNA LT - Ribo-Zero Gold (RS-122-2301/2).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Description |
Beko_DMSO_1
|
| Data processing |
Quality control of FASTQ files was done using fastqc.
Removal of low-quality reads was done using fastx-toolkit.
Read mapping was done using Bowtie2 called from Tophat based on Illumina iGenome mm9 UCSC gene GTF gene definitions.
Mapped reads per gene were extracted using the summarizeOverlaps from the genomicAlignments package in R on Illumina iGenome mm9 UCSC gene definitions.
The extracted read counts were analyzed with DESeq2 in order to obtain expression measures and differential gene expression measures.
Genome_build: mm9
Supplementary_files_format_and_content: Differential gene expression analysis summary from DESeq2 in tabular form.
|
| |
|
| Submission date |
Oct 30, 2017 |
| Last update date |
Feb 04, 2020 |
| Contact name |
Marek Bartkuhn |
| E-mail(s) |
marek.bartkuhn@gen.bio.uni-giessen.de
|
| Organization name |
Justus-Liebig-University Giessen
|
| Department |
Biomedical Informatics and Systems Medicine
|
| Street address |
Aulweg 132
|
| City |
Giessen |
| State/province |
Hessen |
| ZIP/Postal code |
35392 |
| Country |
Germany |
| |
|
| Platform ID |
GPL18480 |
| Series (1) |
| GSE106361 |
Differential Notch target genes expression profile upon HDAC3 loss-of-function. |
|
| Relations |
| BioSample |
SAMN07957917 |
| SRA |
SRX3344845 |
