|
| Status |
Public on Aug 28, 2018 |
| Title |
H3K27me3_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: H3K27me3 (mouse monoclonal; CMA323)
|
| 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 |
SAMN08743493 |
| SRA |
SRX3824808 |
