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Sample GSM8438153 Query DataSets for GSM8438153
Status Public on Nov 04, 2024
Title ExpiCHO-S
Sample type SRA
 
Source name Ovary
Organism Cricetulus griseus
Characteristics tissue: Ovary
cell line: ExpiCHO-S
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 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 SAMN43012575
SRA SRX25588135

Supplementary file Size Download File type/resource
GSM8438153_ExpiCHO-S_cov.bed.gz 186.1 Mb (ftp)(http) BED
GSM8438153_ExpiCHO-S_ratio.bed.gz 192.5 Mb (ftp)(http) BED
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Raw data are available in SRA

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