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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Mar 24, 2021 |
| Title |
adipocyte WT (Bisulfite-Seq) |
| Sample type |
SRA |
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| Source name |
adipocytes
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: epididymal adipose tissue
cell type: adipocytes
age: 17wks old
genotype: wild type
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Briefly, primary adipocytes were lysed for 1 h in lysis buffer at 37°C and digested with 10 g/mL proteinase K for 3 h at 50°C. After cell lysis, DNA and RNA was isolated by phenol-chloroform extraction and using trizol, respectively.
For WGBS library construction, 100ng of genomic DNA was treated with the EZ DNA Methylation-Gold kit (Zymo Research, Orange, CA, USA) for bisulfite conversion. Then, the sequencing libraries were prepared according to the manufacturer’s instructions of TruSeq DNA Methylation Library Preparation Kits (Illumina, #EGMK91396). Briefly, bisulfite-converted DNA is random-primed using a polymerase to synthesize DNA containing a specific sequence tag. The 3’ ends of the newly synthesized DNA strands are tagged with a second specific sequence. The di-tagged DNA molecules are amplified using FailSafe PCR Enzyme (Epicentre, #FSE51100) and TruSeq Index PCR Primer. The final purified product is quantified using qPCR according to the qPCR Quantification Protocol Guide and qualified using the Agilent Technologies 2100 Bioanalyzer (Agilent). Finally, sequencing was performed using the HiSeqX platform (Illumina). In case of RNA-seq, RNA libraries were prepared for sequencing using standard Illumina protocols.
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
HiSeq X Ten |
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| Description |
WT
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| Data processing |
For WGBS data, sequenced reads were trimmed with adaptor sequences and performed quality control using TrimGalore v0.5.0. Then, the trimmed reads were mapped to the mouse genome (GRCm38) using Bismark v0.22.1. Cytosines that were mapped less than five reads were discarded for downstream analyses. Methylation levels of individual CpGs were determined using Bismark Methylation Extractor.
For RNA-seq data, Sequenced reads of adipocytes were trimmed with adaptor sequences and performed quality control by using trim galore. The trimmed reads were mapped to the mouse genome (GRCm38) using Rsubread v2.0.1. Raw read counts per genes were measured using featurecounts program in Rsubread with the builid-in mouse genome annotation (GRCm38).
Genome_build: mm10
Supplementary_files_format_and_content: wig files include CpG methylation values for each sample
Supplementary_files_format_and_content: Excel file include FPKM values for every genes and every adipocyte WT replicates.
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| Submission date |
Oct 02, 2020 |
| Last update date |
Mar 24, 2021 |
| Contact name |
Yoon Jeong Park |
| Organization name |
Seoul National University
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| Street address |
San 56-1, Sillim-Dong, Gwanak-Gu
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| City |
Seoul |
| ZIP/Postal code |
08826 |
| Country |
South Korea |
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| Platform ID |
GPL21273 |
| Series (1) |
| GSE158944 |
Genome-wide maps of Dnmt1-dependent DNA methylome in adipocytes |
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| Relations |
| BioSample |
SAMN16351969 |
| SRA |
SRX9235834 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4816109_WT_CG_met_cov5.BEDGRAPH.gz |
178.7 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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