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Sample GSM1432930 Query DataSets for GSM1432930
Status Public on Oct 01, 2015
Title Exp1 C2 iMEFs Ezh2 -/-, replicate 1
Sample type SRA
 
Source name C2 iMEFs Ezh2 -/-
Organism Mus musculus
Characteristics cell type: iMEFs
antibody: H3K27me3 ChIP (Active Motif 39155)
Treatment protocol 4-hydroxytamoxifen was used at a final concentration ranging from 1 nM to 1 μM
Growth protocol Sample 1 to 16 iMEF cells grown in DMEM medium supplemented with 10% FCS, 100 mM non essential amino acids, 1 mM L-Glutamine.
Extracted molecule genomic DNA
Extraction protocol DNA was extracted by phenol-chloroform and precipitated. Experiment 1 : Sequencing was performed on SOLiD 5500 single reads 75bp. Experiment 2 : Sequencing was performed on Hi-Seq 2500 Illumina single reads 100bp.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model AB 5500 Genetic Analyzer
 
Data processing Experiment 1 : Single-end reads were mapped on the Mouse reference genome (mm9) Using the Bowtie software (v0.12.8, Langmead B. Et al. 2012) Allowing one mismatch in the seed (28bp) And reporting one location in case of multiple mapping hits.
Experiment 1 : Peak calling for each sample was done with MACS2 2.0.10 with default parameters for histone analysis, By specifying a fragment size of 150bp and the Input DNA as Control.
Experiment 2 : Single-end 100bp reads were mapped on the Mouse reference genome (mm9) Using the Bowtie2 software (v2.1.0, Langmead B. Et al. 2012) Allowing one mismatch in the seed (22bp) And reporting one location in case of multiple mapping hits.
Experiment 2 : PCR duplicates were then removed using samtools
Experiment 2 : Peak calling for each sample was done with CCAT 3.0 with default parameters for histone analysis, By specifying a fragment size of 150bp and the Input DNA BAM file as Control.
Genome_build: mm9
Supplementary_files_format_and_content: bed files are the output of peak calling.
Supplementary_files_format_and_content: BigWig files are generated with HOMER (v3.17)
 
Submission date Jul 10, 2014
Last update date May 15, 2019
Contact name Nicolas Servant
E-mail(s) Nicolas.Servant@curie.fr
Organization name Institut Curie
Street address 26 rue d'ulm
City Paris Cedex 05
ZIP/Postal code 75248
Country France
 
Platform ID GPL16790
Series (2)
GSE59293 Genome-wide analysis of H3K27me3 in Ezh2-conditional iMEFs
GSE59427 Impaired PRC2 activity promotes transcriptional instability and favors breast tumorigenesis
Relations
BioSample SAMN02911606
SRA SRX652240

Supplementary file Size Download File type/resource
GSM1432930_S20C4.bigWig 211.0 Mb (ftp)(http) BIGWIG
GSM1432930_S20C4_peaks.bed.gz 294.1 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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