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Sample GSM4103900 Query DataSets for GSM4103900
Status Public on Dec 02, 2019
Title WT_H3K27me3 ChIP-seq rep2
Sample type SRA
 
Source name WT_H3K27me3
Organism Mus musculus
Characteristics cell type: Embryonic stem cells
genotype/variation: vector control
chip antibody: H3K27me3
chip antibody info.: Diagenode #C15410195-10
Treatment protocol mESC are stably transfected with ppy-cagg-ires-puro vector epty or encoding a netrin-1 transgene.
Growth protocol mESC are grown in serum/LIF conditions
Extracted molecule genomic DNA
Extraction protocol ChIP-seq is performed as previously described (Galonska et al., Cell Stem cell 2015)
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
 
Data processing BWA was used for alignment of data to the mm9 genome with de-duplication performed using Picard tools, followed by peak calling using macs2 with narrow peak settings. To compare between control and netrin-1 conditions, homer annotatePeaks.pl was used with size = 2000, hist = 10 and –ghist used to generate read enrichments from both the control and netrin-1 sample using the control macs2 peaks. Data was then plotted in R using custom scripts
Genome_build: mm9
Supplementary_files_format_and_content: Coverage files used to plot the density composites for bivalent genes in figure 3k. Both for H3K27me3 and H3K4me3. Both text files output from Homer AnnotatePeaks after creating tag directories with the bam files.
 
Submission date Oct 01, 2019
Last update date Dec 02, 2019
Contact name Fabrice Lavial
Organization name CRCL
Street address 28 rue Laennec
City Lyon
ZIP/Postal code 69008
Country France
 
Platform ID GPL19057
Series (2)
GSE102831 Netrin-1 signalling function in mouse pluripotent stem cells
GSE105062 Netrin-1 signalling function in mouse pluripotent stem cells [ChIP-Seq]
Relations
BioSample SAMN12880817
SRA SRX6931132

Supplementary file Size Download File type/resource
GSM4103900_WT_H3K27me3_rep2_mm9_RPKM.bw 103.4 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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