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Sample GSM5825480 Query DataSets for GSM5825480
Status Public on Jul 07, 2022
Title RNA-seq in Beko cells, USP10_KD_2
Sample type SRA
 
Source name Beko pre-T cell line
Organism Mus musculus
Characteristics cell line: Beko
cell type: pre-T cells
treatment: infected with plasmids driving the expression of shRNAs against Usp10
Treatment protocol Mouse pre-T (Beko) cells were treated for 24 hours with 0.5 mM DMOG or DMSO as a control. Alternatively, Beko cells were kept for 12 hours at 1% oxygen to induce hypoxia or at 5% oxygen as a 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 RNA-Seq samples were prepared essentially as as previously described (Giaimo et al. NAR 2018, doi: 10.1093/nar/gky551)
Illumina TruSeq Stranded Total RNA Sample Preparation kit.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description RNA_Seq_Counts.xlsx
Data processing Quality control of FASTQ files was done using the seeFastq command within systemPipeR.
The fastq files were aligned using TopHat v.2.1.1. or Hisat2 v.2.2.1
Count tables were generated from BAM files using the summarizeOverlaps function.
ChIP-seq aligment was performed using Bowite 2 v.2.3.5.1.
Duplicated reads were removed using Picard tools.
bigWig files were generated using bamCoverage.
Peak calling was done using Peakranger v.1.18 and followed by MSPC to combine peak sets.
Genome_build: mm9
Supplementary_files_format_and_content: RNA-seq: Count tables of raw read counts per gene in csv format.
Supplementary_files_format_and_content: ChIP-seq: bigWig files.
 
Submission date Jan 19, 2022
Last update date Jul 07, 2022
Contact name Tobias Friedrich
E-mail(s) tobias.friedrich@pennmedicine.upenn.edu
Organization name University of Pennsylvania
Street address 421 Curie Boulevard
City Philadelphia
State/province Pennsylvania
ZIP/Postal code 19104
Country USA
 
Platform ID GPL24247
Series (1)
GSE194003 Characterization of the crosstalk between Notch signaling and hypoxia
Relations
BioSample SAMN25122611
SRA SRX13832290

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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