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Sample GSM3057419 Query DataSets for GSM3057419
Status Public on Aug 28, 2018
Title Input_WT
Sample type SRA
 
Source name E13.5 MEF
Organism Mus musculus
Characteristics developmental stage: E13.5
cell type: mouse embryonic fibroblasts
genotype: Smchd1 +/+
strain: C57BL6/J
Sex: female
chip antibody: none
Extracted molecule genomic DNA
Extraction protocol ChIP was performed as described by Nozawa et al., (2013)
ChIP-seq libraries were prepared as described by Nozawa et al., (2013)
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer IIx
 
Description H3K27me3enrichment.txt.gz
Data processing Data processing of ChIP-seq was performed as described by Nozawa et al., (2013) with minor modifications. The sequence reads were aligned to the mouse reference genome (UCSC mm9, without Y chromosome) and a single unit of mouse ribosomal DNA repeats (BK000964.1).
We calculated the H3K27me3 enrichment values defined as log2([ChIP RPKM]/[Input RPKM]) in each gene body. Genes with their length ≤ 1 kb or Input RPKM < 0.1 were excluded due to low read counts.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file include H3K27me3 enrichment values defined as log2([ChIP RPKM]/[Input RPKM]) for each genotype
 
Submission date Mar 20, 2018
Last update date Aug 28, 2018
Contact name Koji Nagao
E-mail(s) nagao@bio.sci.osaka-u.ac.jp
Organization name Osaka University
Department Graduate School of Science
Lab Obuse Lab.
Street address 1-1 Machikaneyama
City Toyonaka
State/province Osaka
ZIP/Postal code 560 0043
Country Japan
 
Platform ID GPL11002
Series (2)
GSE112096 Role of SmcHD1 in the establishment of the epigenetic states required for the maintenance of X chromosome inactivation [ChIP-seq]
GSE112097 Role of SmcHD1 in the establishment of the epigenetic states required for the maintenance of X chromosome inactivation
Relations
BioSample SAMN08743494
SRA SRX3824807

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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