|
| Status |
Public on Mar 23, 2022 |
| Title |
WGBS_Hsap_fibro |
| Sample type |
SRA |
| |
|
| Source name |
Primary dermal fibroblasts
|
| Organism |
Homo sapiens |
| Characteristics |
Sex: Female
genome build: hg38
treatment: No treatment
tissue: Primary dermal fibroblasts
|
| Growth protocol |
Primary dermal fibroblasts were grown in DMEM-GlutaMax supplemented with 10% fetal bovine serum and 50U/mL penicillin-streptomycin in a humidified atmosphere containing 5% CO2 at 37°C.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted using the AllPrep DNA/RNA Mini Kit (Qiagen).
100 ng of genomic DNA were fragmented to 350 bp using a Covaris E220 sonicator. Bisulfite conversion was performed with the EZ DNA Methylation-Gold kit (Zymo), and WGBS libraries were prepared using the Accel-NGS Methyl-Seq DNA library Kit (Swift Biosciences) following the manufacturer’s instructions. 4 to 6 cycles were used for the final PCR amplification of the WGBS libraries. The libraries were purified using Agencourt AmpureXP beads (Beckman-Coulter).
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Low quality bases as well as the first five bases of reads R1 and ten bases of reads R2 and adapter sequences were trimmed with Trim Galore v0.4.4 (parameters -q 20 --clip_R1 5 --clip_R2 10 --stringency 2).
Reads were mapped to the corresponding genome and cleaned for duplicates using Bismark v0.22.1 with default parameters. Reads with incomplete bisulfite conversion were removed using the filter_non_conversion tool in Bismark with the parameters --minimum_count 5 and --percentage_cutoff 50
Reads with incomplete bisulfite conversion were removed using the filter_non_conversion tool in Bismark v0.22.1 with the parameters --minimum_count 5 and --percentage_cutoff 50
Methylation calls were extracted as the ratio of the number of Cs over the total number of Cs and Ts using the Bismark_methylation_extractor. CGs were filtered to have a minimum sequencing depth of 5X.
genome build: hg38, mm10, oryCun2, canFam3, bosTau8, susScr11, galGal6
processed data files format and content: We provide IGV files containing methylation scores for all CGs with at least 5X sequencing depth.
|
| |
|
| Submission date |
May 27, 2021 |
| Last update date |
Mar 23, 2022 |
| 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 |
GPL20301 |
| Series (1) |
| GSE175615 |
Conservation and divergence of DNA methylation patterns and functions in vertebrates |
|
| Relations |
| BioSample |
SAMN19365316 |
| SRA |
SRX11003179 |
