|
| Status |
Public on Mar 01, 2013 |
| Title |
Dnmt1+/+ MEF (Bisulfite-seq) |
| Sample type |
SRA |
| |
|
| Source name |
Dnmt1+/+ mouse embryonic fibroblasts
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Mouse embryonic fibroblasts
strain: see Lande-Diner 2007 (PMID: 17311920)
genotype/variation: Dnmt1+/+
|
| Treatment protocol |
Not applicable
|
| Growth protocol |
Mouse embryonic fibroblasts were cultured under standard conditions
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was isolated by cell lysis and Proteinase K digestion followed by phenol-chloroform extraction. RNA was removed by Rnase treatment.
Bisulfite-converted DNA libraries were prepared by BaseClear (Leiden, Netherlands) according to their 'EpiQuest Genome-wide' service
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
Reduced Representation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
fastq files are split into two sets of paired end files
|
| Data processing |
Base calling was performed by BaseClear according to their 'Epiquest Genome-wide' service
Reads were mapped to the bisulfite converted genome using Bismark by BaseClear according to their 'Epiquest Genome-wide' service
For each CpG covered by sequencing reads the proportion of unmethylated C and methylated C were determined by the frequency of conversion of C to T. Only CpGs with a sequencing depth greater than 10 were used.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text. A matrix with the following columns: chr (chromosome); start (start coordinate of CpG); stop (stop coordinate of CpG); wt_depth (number of reads that cover this CpG in Dnmt1+/+); wt_meth_percent (proportion of methyl-cytosine as a percentage of total cytosine in Dnmt1+/+); ko_depth (number of reads that cover this CpG in Dnmt1-/-); ko_meth_percent (proportion of methyl-cytosine as a percentage of total cytosine in Dnmt1-/-)
|
| |
|
| Submission date |
Feb 28, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
James P Reddington |
| Organization name |
EMBL
|
| Street address |
Meyerhofstrasse 1
|
| City |
Heidelberg |
| ZIP/Postal code |
69115 Heidelberg |
| Country |
Germany |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE44278 |
Redistribution of H3K27me3 upon DNA hypomethylation results in de-repression of polycomb-target genes |
| GSE44760 |
Reduced Representation Bisulfite Sequencing in DNA methylation deficient mouse embryonic fibroblasts |
|
| Relations |
| SRA |
SRX246877 |
| BioSample |
SAMN01933052 |
