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Sample GSM8435093 Query DataSets for GSM8435093
Status Public on Nov 04, 2024
Title Day0_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) [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)
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 SAMN42955547
SRA SRX25535795

Supplementary file Size Download File type/resource
GSM8435093_BR2_D0_cov.bed.gz 183.6 Mb (ftp)(http) BED
GSM8435093_BR2_D0_ratio.bed.gz 186.2 Mb (ftp)(http) BED
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