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Sample GSM2836571 Query DataSets for GSM2836571
Status Public on Feb 04, 2020
Title Beko_SCR_rep1
Sample type SRA
Source name Beko_SCR
Organism Mus musculus
Characteristics cell type: pre-T cells (Beko)
infected with: plasmids driving the expression of scrambled (SCR) shRNAs as control.
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_Scr_96h_post-puro_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
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.
BioSample SAMN07957913
SRA SRX3344849

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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