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Sample GSM3715060 Query DataSets for GSM3715060
Status Public on Aug 30, 2019
Title WGBS_mESC_NSD1_KO
Sample type SRA
 
Source name Mouse embryonic stem cells
Organism Mus musculus
Characteristics strain: C57BL/6 x 129S4/SvJae
cell line: ESC line V6.5 1A
cell type: C57BL/6 x 129S4/SvJae F1 embryo-derived embryonic stem cells
genotype: sgNSD1
Growth protocol Mouse embryonic stem cells were maintained on gelatin-coated plates in Knockout DMEM (Gibco) supplemented with 15% ES-cell-qualified FBS (Gemini), 0.1 mM 2-mercapoethanol, 2mM L-glutamine (Life technologies) and LIF.
Extracted molecule genomic DNA
Extraction protocol DNA was extracted from flash frozen cell pelets of about 5 million cells using DNeasy Blood & Tissue Kit from QIAGEN Cat. #69506
NxSeq AmpFREE Low DNA Library Kit (Lucigen). Samples were then bisulfite converted using the EZ-DNA Methylation Gold Kit (Zymo Research). DNA was amplified by 9 cycles of PCR using the Kapa Hifi Uracil + DNA polymerase (KAPA Biosystems).
 
Library strategy Bisulfite-Seq
Library source genomic
Library selection RANDOM
Instrument model HiSeq X Ten
 
Data processing Raw reads from whole-genome bisulfite sequencing were aligned using BWA (version 0.6.1). Low-quality sequence at the 3′ ends were trimmed. After alignment, we filtered duplicated or poorly mapping reads (>2% mismatches or aberrant insert size). Samtools (version 0.1.18) in mpileup mode was applied to call CpG methylation. We filtered CpGs with less than 5x coverage, overlapping with SNPs from dbSNPs (build 137) or located within the ENCODE DAC blacklisted regions or Duke excluded regions.
Genome_build: mm10
Supplementary_files_format_and_content: tdf
 
Submission date Apr 09, 2019
Last update date Aug 30, 2019
Contact name Carmen Rivas
E-mail(s) mcarmen.rivas@usc.es
Organization name Universidad de Santiago de Compostela
Department CIMUS
Lab P2L7
Street address Avda Barcelona
City Santiago de Compostela
ZIP/Postal code 15706
Country Spain
 
Platform ID GPL21273
Series (1)
GSE118785 H3K36me2 recruits DNMT3A and shapes intergenic DNA methylation landscapes
Relations
BioSample SAMN11373149
SRA SRX5657610

Supplementary file Size Download File type/resource
GSM3715060_mESC_sgNSD1_BS_1-mm10_CpG.tdf 196.7 Mb (ftp)(http) TDF
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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