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Sample GSM1858319 Query DataSets for GSM1858319
Status Public on Jan 05, 2017
Title H3K27me3_WT_rep1
Sample type SRA
 
Source name Mouse embryonic fibroblasts
Organism Mus musculus
Characteristics genotype: Rnf40+/+
passages: 3
chip antibody: H3K27me3 (Diagenode, pAb-195-050)
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 genomic DNA
Extraction protocol Cells were crosslinked with 1% Formaldehyde for 10 minutes and quenched with 1.25 M Glycine. The nuclear pellets were sonicated to the fragment range of 200-400 bp. Sonicated extracts were incubated with specific antibodies at 4˚C overnight and ChIP-immune complexes were pulled down using Protein A sepharose.
Library preparations were done using NEBnext Ultra DNA library preparation kit according to the manufacturer’s instructions.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2500
 
Data processing ChIP-seq reads were aligned to the mm9 genome assembly using bowtie version 1.0.0
peaks were called using MACS version 1.0.0 with the following setting: Effective Genome Size (Mouse (mm9)), Tag size (25), Bandwidth (300), Pvalue (0.00001), Shift size (125).
Coverage was determined by normalizing the filtered reads per hundred million
bigwig files were generated using Wig/BedGraph-to-bigWig
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files were generated from wig files using Wig/BedGraph-to-bigWig
 
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 GPL17021
Series (2)
GSE72237 Genome-wide H2B monoubiquitination regulates gene expression by coordinating H3K4me3 and H3K27me3 [ChIP-Seq Data Set]
GSE72239 Genome-wide H2B monoubiquitination regulates gene expression by coordinating H3K4me3 and H3K27me3
Relations
BioSample SAMN04003021
SRA SRX1160445

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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