|
| Status |
Public on Nov 04, 2024 |
| Title |
Day5_timeseries_replicate2 |
| Sample type |
SRA |
| |
|
| Source name |
Ovary
|
| Organism |
Cricetulus griseus |
| Characteristics |
tissue: Ovary
cell line: CHO-K1
cell type: Chinese hamster ovary (CHO) cells
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted using the PureLink Genomic DNA Isolation Minikit kit (Invitrogen), including RNAase treatment following the manufacturer's instructions
Libraries for whole-genome bisulfite sequencing (WGBS) were prepared using the VAHTS Universal Pro DNA Library Prep Kit for Illumina (Vazyme, Catalog #ND608).
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Reads were trimmed using Trimmomatic and mapped with BSMAP version 2.9. The assembly of Cricetulus_griseus CHOK1GS_HDv1.108 was used as genome reference. Duplicate reads were removed using the Picard tool (http://broadinstitute.github.io/picard).
Methylation ratios were determined using a Python script (methratio.py) that is distributed with the BSMAP package. For all further analysis, only CpGs covered by at least five reads were considered.
Assembly: Cricetulus_griseus CHOK1GS_HDv1.108
Supplementary files format and content: BED files containing CpGs with information about coverage (_cov) and methylation ratios (_ratio)
|
| |
|
| Submission date |
Jul 31, 2024 |
| Last update date |
Nov 04, 2024 |
| Contact name |
Elias Böhl |
| E-mail(s) |
elias.boehl@dkfz-heidelberg.de
|
| Organization name |
German Cancer Research Center (DKFZ)
|
| Department |
Divison of Epigenetics
|
| Street address |
Im Neuenheimer Feld 580
|
| City |
Heidelberg |
| ZIP/Postal code |
69120 |
| Country |
Germany |
| |
|
| Platform ID |
GPL27425 |
| Series (2) |
| GSE273684 |
Analysis of population heterogeneity in CHO cells by genome-wide DNA methylation analysis and by multi-modal single-cell sequencing [time series] |
| GSE273685 |
Analysis of population heterogeneity in CHO cells by genome-wide DNA methylation analysis and by multi-modal single-cell sequencing |
|
| Relations |
| BioSample |
SAMN42955541 |
| SRA |
SRX25535801 |
