|
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).
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|
|
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
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|
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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 |