|
| Status |
Public on May 20, 2020 |
| Title |
WGBS_D1KO_Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
E8.5 whole embryos
|
| Organism |
Mus musculus |
| Characteristics |
strain background: C57BL/6J
genotype/variation: Dnmt1-/-
developmental stage: E8.5
gender: Female
tissue: whole embryos
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted with the AllPrep DNA/RNA Mini Kit (Qiagen).
50 ng of genomic DNA were fragmented to 350 bp using a Covaris E220 sonicator. DNA was bisulfite-converted with the EZ DNA Methylation-Gold kit (Zymo Research) and WGBS libraries were prepared using the Accel-NGS Methyl-Seq DNA Library Kit (Swift Biosciences) according to the manufacturer's instructions with 7 PCR cycles for the final amplification. The libraries were purified using Ampure XP beads (Beckman Coulter).
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Reads were cleaned to remove low quality bases as well as the first five bases of reads R1 and ten bases of reads R2 with Trim Galore v0.4.2 using the parameters --paired -q 20 --stringency 2 --clip_R1 5 --clip_R2 10. The reads were aligned to the mm10 genome and cleaned for duplicates using Bismark v0.22.1 with default parameters. Reads with signs of incomplete conversion were removed using the filter_non_conversion option in Bismark with the parameters --minimum_count 5 and --percentage_cutoff 50. Methylation calls were extracted using the Bismark methylation extractor. CGs were filtered to have a minimum sequencing depth of 5X 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 5X 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 |
GPL21103 |
| Series (1) |
| GSE130735 |
Genome-wide roles of DNA methyltransferases in mouse embryos |
|
| Relations |
| BioSample |
SAMN14945086 |
| SRA |
SRX8357966 |
