|
Status |
Public on Nov 04, 2024 |
Title |
Humira431 |
Sample type |
SRA |
|
|
Source name |
Ovary
|
Organism |
Cricetulus griseus |
Characteristics |
tissue: Ovary cell line: Humira431 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).
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|
|
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).
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|
|
Submission date |
Aug 02, 2024 |
Last update date |
Nov 04, 2024 |
Contact name |
Elias Böhl |
E-mail(s) |
[email protected]
|
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) |
GSE273685 |
Analysis of population heterogeneity in CHO cells by genome-wide DNA methylation analysis and by multi-modal single-cell sequencing |
GSE273851 |
Analysis of population heterogeneity in CHO cells by genome-wide DNA methylation analysis and by multi-modal single-cell sequencing [WGBS] |
|
Relations |
BioSample |
SAMN43012572 |
SRA |
SRX25588138 |