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| Status |
Public on Jun 24, 2024 |
| Title |
WGBS_Human_PrimedESCs_Rep1 |
| Sample type |
SRA |
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| Source name |
Human embryonic stem cells
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| Organism |
Homo sapiens |
| Characteristics |
cell line: Human embryonic stem cells
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA (gDNA) was extracted from hESCs by using DNeasy Blood & Tissue Kits (Qiagen, Cat# 69504) according to the manufacturer’s protocol.
200 ng of purified gDNA of hESC was subjected to bisulfite conversion and purification by using the EZ-96 DNA Methylation-Direct MagPrep kit (Zymo Research, Cat# D5045) according to the manufacturer’s protocol. Then, WGBS libraries were constructed via our recently published TAILS method. In brief, P5-N6-oligo1 (5’-CTACACGACG-CTCTTCCGATCTN6-3’) was used for the first round of random priming in the presence of the Klenow exo(-) fragment. The remaining oligos and dNTPs were removed by Exo-SAP IT Express, and the dC tailing step was performed with the TdT enzyme. Then, a second round of priming was conducted by using P7-G6-oligo2 (5’-AGACGTGTGCTCTTCCGATCTG6HN-3’) in the presence of the Klenow exo(-) fragment. After one round of purification with AMPure XP beads, libraries were constructed by PCR amplification. Next, the libraries were purified, and the size distribution was checked on the fragment analyzer. Finally, the WGBS libraries were sequenced on a NovaSeq 6000 sequencer with a 150 bp paired-end sequencing strategy.
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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 |
Raw 150 bp paired-end reads were trimmed using TrimGalore (v0.6.6) with the following parameters: --quality 20 --stringency 3 --length 50 --clip_R1 9 --clip_R2 9 --paired --trim1 --phred33. Adapters and low-quality reads were filtered out. The remaining reads were aligned to the reference genome (UCSC version hg19) using Bismark (v0.23.1). The alignment process was carried out in paired-end mode initially, followed by two independent rounds of alignment in single-end mode for unmapped Read1 and Read2. The deduplication of the resulting reads was performed using sambamba markup (v0.8.2), and the function filter_non_conversion in Bismark was utilized to filter out reads with three consecutive nonconversion sites. The remaining reads were then subjected to downstream analysis. MethylDackel (v0.5.0) was used to extract and count cytosines in the CpG sequence context.
Assembly: hg19
Supplementary files format and content: bedGraph, CpGs methylation levels. Column 4 for unmethylated C (T), Column 5 for methylated C (C), Column 6 for CpG methylation level, which is defined as C/(C + T).
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| Submission date |
Jun 20, 2024 |
| Last update date |
Jun 24, 2024 |
| Contact name |
Fan Guo |
| E-mail(s) |
[email protected]
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| Organization name |
Institute of Zoology, Chinese Academy of Sciences
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| Department |
The State Key Laboratory of Stem Cell and Reproductive Biology
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| Lab |
Group of Reproductive Epigenetics
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| Street address |
1 Beichen West Road, Chaoyang District
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| City |
Beijing |
| State/province |
Beijing |
| ZIP/Postal code |
100101 |
| Country |
China |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE224618 |
Divergent originations of parental DNA hydroxymethylation in human preimplantation embryos |
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| Relations |
| BioSample |
SAMN41940673 |
| SRA |
SRX24993274 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8342379_WGBS_Human_PrimedESCs_Rep1_CpG.bedGraph.gz |
201.4 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
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