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Sample GSM1858332 Query DataSets for GSM1858332
Status Public on Jan 05, 2017
Title Rnf40_WT_rep2
Sample type SRA
 
Source name mouse embryonic fibroblasts
Organism Mus musculus
Characteristics genotype: Rnf40+/+
passages: 3
Treatment protocol For RNF40 knockout, MEFs were passaged into GlutaMAX™-DMEM supplemented with 250nM of 4-hydroxitamoxifen (4-OHT) for 5 days, and then cultured for 3 days without 4-OHT.
Growth protocol Primary MEFs were cultured in high-glucose GlutaMAX™-DMEM (Invitrogen) supplemented with 10% FBS Superior (Biochrom), 1% penicillin–streptomycin (Sigma-Aldrich), and 1% non-essential amino acids (Invitrogen) at 37°C, 5% CO2.
Extracted molecule total RNA
Extraction protocol total RNA was isolated using QIAzol Lysis Reagent (QIAGEN)
Libraries were prepared from 1 µg of total RNA using NEXTflex™ Rapid Directional RNA-Seq Kit according to the manufactures introduction (Bioo Scientific).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Data processing Sequenced reads were mapped to mouse reference transcriptome (UCSC mm9) using bowtie 2 (version 2.1.0) with parameters --threads 11 --very-sensitive --omit-sec-seq
Read counts for each sample and each gene were aggregated using a custom Ruby script
DESeq (version 1.14.0) was used for measuring differential expression
Genome_build: mm9
Supplementary_files_format_and_content: The table includes gene normalized counts for each sample
 
Submission date Aug 20, 2015
Last update date May 15, 2019
Contact name Steven A Johnsen
E-mail(s) steven.johnsen@med.uni-goettingen.de
Organization name University Medical Center Göttingen
Department Clinic for General, Visceral and Pediatric Surgery
Lab AG Tumorepigenetics
Street address Robert Koch Strasse 40
City Göttingen, Niedersachsen
State/province Niedersachsen
ZIP/Postal code 37075
Country Germany
 
Platform ID GPL13112
Series (2)
GSE72238 Genome-wide H2B monoubiquitination regulates gene expression by coordinating H3K4me3 and H3K27me3 [RNA-Seq Data Set]
GSE72239 Genome-wide H2B monoubiquitination regulates gene expression by coordinating H3K4me3 and H3K27me3
Relations
BioSample SAMN04003034
SRA SRX1160458

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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