 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Sep 04, 2019 |
| Title |
LR1 |
| Sample type |
SRA |
| |
|
| Source name |
muscle tissue
|
| Organism |
Sus scrofa |
| Characteristics |
breed: Landrance
Stage: 18 dpc
tissue: longissimus dorsi muscle
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Total Genomic DNA (gDNA) were extracted from the same frozen tissue samples by using the All Prep DNA Mini Kit (Qiagen, Valencia, CA, USA) according to the manufacturer’s protocol. DNA concentration was detected by NanoDrop spectrophotometer and quality was assessed by 1% agarose gel by electrophoresis.
DNA was fragmented by using sonication into 100-500 bp in size, and then followed by end blunting, dA addition at the 3’end and ligation of adapters. The adapter sequence had multiple methyl cytosines so as to allow monitoring of the bisulfite conversion efficiency. Unmethylated cytosines were converted to uracils after bisulfite treatment by a modified protocol from previously described. DNA fragments with size range of 320 to 380 bp were gel-purified for sequencing. All procedures were carried out by the manufacturer’s instructions. Converted DNA was subjected to 50 bp paired end sequencing by Illumina Solexa GA sequencer (Illumina, San Diego, CA, USA). All the raw data was processed by the Illumina Pipeline v1.3.1 (Illumina, San Diego, CA, USA).
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
miniature pig
|
| Data processing |
The remaining clean reads were then aligned to Sus scrofa reference genome build 10.23 by using SOAP aligner v2.21 (http://soap.genomics.org.cn/)
Annotation information of the porcine reference genome was obtained from the Ensembl public FTP site (ftp://ftp.ensembl.org/pub/release-78/gtf/sus_scrofa/Sus_scrofa.Sscrofa10.2.78.gtf.gz)
Genome_build: Sus scrofa reference genome build 10.23
Supplementary_files_format_and_content: wig files were generated using default settings35. Wig files are included in tar archives.
|
| |
|
| Submission date |
Sep 04, 2018 |
| Last update date |
Sep 05, 2019 |
| Contact name |
Delin Mo |
| E-mail(s) |
wangxy635@mail2.sysu.edu.cn
|
| Organization name |
Sun Yat-sen University
|
| Street address |
Xingang Road
|
| City |
Guangzhou |
| ZIP/Postal code |
510006 |
| Country |
China |
| |
|
| Platform ID |
GPL9126 |
| Series (1) |
| GSE119459 |
WGBS analysis of Landrance and Wuzhishan miniature pig |
|
| Relations |
| BioSample |
SAMN09954027 |
| SRA |
SRX4639714 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3374917_LR18_processed_data.tar.gz |
217.8 Mb |
(ftp)(http) |
TAR |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
