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| Status |
Public on Sep 01, 2020 |
| Title |
WGBS of Sus scrofa: skeletal muscle at D180, replicate2 |
| Sample type |
SRA |
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| Source name |
skeletal muscle
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| Organism |
Sus scrofa |
| Characteristics |
strain: Landrance
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Total DNA for WGBS was extracted and fragmented by sonication to 200−300 bp using a Covaris S220 (Covaris, Woburn, MA, USA), followed by end repair and A-ligation. After ligation to cytosine-methylated barcodes, the DNA fragments were treated twice with bisulfite using an EZ DNA Methylation-GoldTM Kit (Zymo Research, Orange, CA, USA).
The libraries were then prepared according to the Illumina standard DNA methylation analysis protocol. The WGBS libraries were sequenced on the Illumina HiSeq X Ten platform (Illumina, CA, USA) and 150-bp paired-end reads were generated.
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
HiSeq X Ten |
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| Data processing |
Illumina Covaris S220 software used for basecalling.
After transforming the Sus scrofa reference genome to a bisulfite-converted version (C-to-T and G-to-A conversion) and then indexing it using bowtie2, the bisulfite-treated clean reads were mapped to the reference genome using the Bismark software (v 0.12.5) was used to perform alignments with default parameters
The sequencing depth and coverage of the methylcytosine were summarized after deletion of the duplicated reads. The methylation level of each CpG site was defined as the number of methylated reads (C) divided by the total number of methylated reads (C) and unmethylated reads (T) at the same positions in the reference genome.
Genome_build: Suscrofa 11.1
Supplementary_files_format_and_content: C_level_result.txt.gz
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| Submission date |
Aug 28, 2020 |
| Last update date |
Sep 01, 2020 |
| Contact name |
Zhonglin Tang |
| E-mail(s) |
tangzhonglin@caas.cn
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| Organization name |
Chinese Academy of Agricultural Sciences
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| Department |
Agricultural Genome Institute at Shenzhen
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| Street address |
No.7, Pengfei road, Dapeng District
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| City |
Shenzhen |
| State/province |
GuangDong |
| ZIP/Postal code |
518100 |
| Country |
China |
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| Platform ID |
GPL22918 |
| Series (2) |
| GSE157043 |
Whole-genome bisulfite sequencing across 27 developmental stages in Sus scrofa skeletal muscle |
| GSE157045 |
27 developmental stages in Sus scrofa skeletal muscle |
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| Relations |
| BioSample |
SAMN10024112 |
| SRA |
SRX4663766 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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