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| Status |
Public on Jun 04, 2024 |
| Title |
mESC_WT_WGBS_rep1 |
| Sample type |
SRA |
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| Source name |
J1
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| Organism |
Mus musculus |
| Characteristics |
cell line: J1
cell type: mESC
genotype: Wildtype
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| Growth protocol |
J1 mouse embryonic stem cells (mESCs) were grown on gelatin-coated plates without feeder cell layers in knockout DMEM supplemented with 15% (v/v) ES-qualified fetal bovine serum (FBS), 1x non-essential amino acids, 2 mM L-glutamine, 100 mM b-mercaptoethanol, and 1,000 U/ml LIF at 37°C in a 5% CO2 standard incubator.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted using a Quick-DNA Miniprep Plus kit (Zymo Research, D4070).
The Accel-NGS Methyl-Seq DNA Library Kit (Swift Biosciences, 30024) was used according to the manufacturer’s instructions to perform bisulfite conversion and library preparation.
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Paired-end reads were trimmed using Trim_Galore(version 0.6.7) with the following parameters : --length 50, --clip_R1 10, --clip_R2 18, --three_prime_clip_R1 10, and --three_prime_clip_R2 10.
Trimmed reads were aligned to the mm10 using Bismark version 0.19.0 and Bowtie2 (v2.3.3.1) with the following parameters: -X 1000, --nucleotide_coverage and --bowtie2.
Duplication were removed using the deduplicate_bismark script provided with Bismark.
CpG methylation values were called by the bismark_methylation_extractor script provided with Bismark and the following parameters: --no_overlap, --comprehensive, --merge_non_CpG, and --cytosine_report.
Methylation of CpG tracks for IGV browser were generated with bigwig tools.
Assembly: mm10
Supplementary files format and content: bigwig, methylation coverage
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| Submission date |
Jun 03, 2024 |
| Last update date |
Jun 04, 2024 |
| Contact name |
Gerd P. Pfeifer |
| Organization name |
Van Andel Research Institute
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| Department |
Center for Epigenetics
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| Lab |
Pfeifer, Gerd
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| Street address |
333 Bostwick Ave. NE.
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| City |
Grand Rapids |
| State/province |
Michigan |
| ZIP/Postal code |
49503 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE268886 |
CXXC5 stabilizes DNA methylation patterns in mouse embryonic stem cells [Bisulfite-Seq] |
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| Relations |
| BioSample |
SAMN41652321 |
| SRA |
SRX24780657 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8302103_mESC_WT_WGBS_rep1.bw |
92.0 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
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