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Sample GSM7114894 Query DataSets for GSM7114894
Status Public on Jun 11, 2024
Title WT_RNA_Rep1
Sample type SRA
 
Source name MEF
Organism Mus musculus
Characteristics cell line: MEF
cell type: mouse embryonic fibroblasts
genotype: WT
Growth protocol MEFs were derived from mixed 129xC57BL/6-strain of ES cells that were immortalized with SV40 large T antigen. USP44 null cells were generated from exon 1 removal. Lentiviral transduction with USP44 cDNA was used to generate resuce cell line. Cells were cultured in DMEM with 10% FBS.
Extracted molecule total RNA
Extraction protocol Total RNA from MEF cells was isolated using QIAzol reagent and processed with RNeasy Plus Mini Kit (Qiagen).
mRNA-seq libraries were prepared using the TruSeq RNA Library Prep Kit (Illumina).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Data processing All steps were performed with default settings unless otherwise denoted
Sequence reads were trimmed with fastx_trimmer (fastx/0.0.14)
Trimmed sequence reads were mapped to mm10 using star/2.7.9a
Read count extraction was performed using htseq/0.9.1 reverse strand option
Assembly: mm10
Supplementary files format and content: tab-deliminted text files include htseq-count values for each sample
 
Submission date Mar 24, 2023
Last update date Jun 11, 2024
Contact name Steven A Johnsen
E-mail(s) Steven.Johnsen@bosch-health-campus.com
Organization name Robert Bosch Center for Tumor Diseases
Street address Auerbachstrasse 112
City Stuttgart
ZIP/Postal code 70376
Country Germany
 
Platform ID GPL21103
Series (2)
GSE228130 USP44 overexpression drives a MYC-like gene expression program in neuroblastoma through epigenetic reprogramming
GSE228132 USP44 overexpression drives a MYC-like gene expression program in neuroblastoma through epigenetic reprogramming
Relations
BioSample SAMN33902980
SRA SRX19765382

Supplementary file Size Download File type/resource
GSM7114894_WT_RNA_Rep1.countsReverse.txt.gz 135.7 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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