|
| Status |
Public on May 20, 2020 |
| Title |
RRBS_MEF_D1cKO_d7_noTam_Rep3 |
| Sample type |
SRA |
| |
|
| Source name |
Mouse Embryonic Fibroblasts
|
| Organism |
Mus musculus |
| Characteristics |
strain background: C57BL/6J
genotype/variation: Dnmt1 L2/L2
developmental stage: E13.5
gender: Male
cell type: Mouse Embryonic Fibroblasts
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted with the AllPrep DNA/RNA Mini Kit (Qiagen).
RRBS libraries were prepared as described in Auclair et al., Genome Biol 15:545 (2014). Briefly, we digested genomic DNA 5 hours with MspI (ThermoFisher Scientific), followed by end-repair and A-tailing with 5 U Klenow-fragment exo- (ThermoFisher Scientific) and ligation to methylated adapters overnight at 16°C with 30 U T4 DNA ligase (ThermoFisher Scientific) in Tango 1X buffer. Fragments between 150 and 400 bp were excised from a 3% agarose 0.5X TBE gel with the MinElute kit (Qiagen) and bisulfite-converted with the EpiTect Bisulfite kit (Qiagen) using two consecutive rounds of conversion. Final RRBS libraries were amplified with 14-16 cycles of PCR. The libraries were purified using Ampure XP beads (Beckman Coulter).
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
Reduced Representation |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Reads were cleaned with Trim Galore v0.4.2 using the parameters --rrbs --paired -r1 30 -r2 30 -q 20 --length 20 --stringency 5 --retain_unpaired. Reads were aligned to the mouse mm10 genome with BSMAP v2.74 using the parameters -v 2 -w 100 -r 1 -x 400 -m 30 -D C-CGG -n 1. Methylation percent values were extracted with methratio.py from BSMAP v2.74 using the parameters -z -u -g. CGs were filtered to have a minimum sequencing depth of 8X using custom developped scripts in R.
Genome_build: mm10
Supplementary_files_format_and_content: IGV files containing methylation scores for all CGs with at least 8X sequencing depth.
|
| |
|
| Submission date |
May 18, 2020 |
| Last update date |
May 24, 2020 |
| Contact name |
Michael Weber |
| Organization name |
CNRS
|
| Department |
UMR7242 Biotechnology and Cell Signalling
|
| Street address |
300 Bd Sebastien Brant
|
| City |
Illkirch |
| ZIP/Postal code |
67412 |
| Country |
France |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE130735 |
Genome-wide roles of DNA methyltransferases in mouse embryos |
|
| Relations |
| BioSample |
SAMN14945076 |
| SRA |
SRX8357976 |
