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Status |
Public on Dec 02, 2019 |
Title |
WT_H3K27me3 ChIP-seq rep2 |
Sample type |
SRA |
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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.
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Growth protocol |
mESC are grown in serum/LIF conditions
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Extracted molecule |
genomic DNA |
Extraction protocol |
ChIP-seq is performed as previously described (Galonska et al., Cell Stem cell 2015)
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|
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Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina NextSeq 500 |
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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.
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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] |
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Relations |
BioSample |
SAMN12880817 |
SRA |
SRX6931132 |