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| Status |
Public on Nov 09, 2016 |
| Title |
Yorkshire_1 |
| Sample type |
SRA |
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| Source name |
Yorkshire_1
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| Organism |
Canis lupus familiaris |
| Characteristics |
group: Control
tissue: skin fibroblast
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was isolated using a DNA QIAGEN QIAamp DNA Mini Kit following the manufacturer’s protocols.
Genomic DNA was sonicated to 200-300 bp using the Covaris S2 system and then the fragmented DNA was end-repaired using a combination of T4 Polynucleotide Kinase and Klenow polymerase .The blunt, phosphorylated ends were treated with Klenow fragment (3’-5’ exo-) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's methylated adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation , the DNA was bisulphite treated using the EZ DNA Methylation-Gold Kit (ZYMO),and then PCR amplified using JumpStart Taq DNA Polymerase (Sigama)
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
Yorkshire_1
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| Data processing |
Genomic DNA from skin fibroblast was extracted, and sequenced by WGBS technology using Illumina HiSeq2000 sequencer.
Raw sequencing data was processed by the Illumina base-calling pipeline. Low-quality reads that contained more than 30% ’N’s or over 50% of the sequence with low quality value (quality value <20) per read were omitted from the data analysis.
The clean reads were aligned to the reference genome using BSMAP software.
The uniquely aligned reads were used for methylation analysis.
Genome_build: canFam2
Supplementary_files_format_and_content: Cout files include chromosome ID,C sites' coordinate, the number of methylated reads and non-methylated reads
Supplementary_files_format_and_content: Cout file format: (1)Chromosome ID (2)Cytosine position (3)+/- Watson/Crick chain (4)Type (CG/CHH/CHG) (5)Base pattern (6)Copy number (7)Methy reads num (8)Nonmethy reads num (9)Expected value
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| Submission date |
Oct 21, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Desheng Gong |
| E-mail(s) |
gds19870718@163.com
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| Organization name |
Agricultural Genomes Institute at Shenzhen
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| Street address |
No.7 PengFei road
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| City |
Shenzhen |
| ZIP/Postal code |
518120 |
| Country |
China |
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| Platform ID |
GPL16540 |
| Series (1) |
| GSE74225 |
Stochastic anomaly of methylome but persistent SRY hypermethylation in disorder of sex development in canine somatic cell nuclear transfer |
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| Relations |
| BioSample |
SAMN04201342 |
| SRA |
SRX1360786 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1914917_Yorkshire_1.cout.txt.gz |
4.7 Gb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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