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| Status |
Public on Jan 17, 2018 |
| Title |
Dog_MLHD_Bis_PCR_27 |
| Sample type |
SRA |
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| Source name |
Buccal
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| Organism |
Canis lupus familiaris |
| Characteristics |
breed: MLHD
tissue: buccal
Sex: M
age: 1.2
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Targeted bisulfite PCR-based analysis was performed using the 48.48 layout on the Fluidigm C1 system (Fluidigm, USA), coupled with Illumina MiSeq sequencing. Bisulfite PCR primers were designed using Primer3 (PMID:17485472),
DNA was bisfulite converted (EpiTect, Qiagen) prior to amplification. Amplicons from a single sample were pooled and individually indexed to create a multiplex library prior to sequencing on an Illumina MiSeq instrument using v3 chemistry.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina MiSeq |
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| Description |
Bis-PCR
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| Data processing |
Library strategy: Bis-PCR
Bismark (v0.13.1) was used to align reads to the reference genome camFam using Bowtie2
Methylation counts were extracted using https://bitbucket.org/lowelabqmul/methylation-extractor
Genome_build: canFam 3.1
Supplementary_files_format_and_content: chromosome,position,methylation count,total count
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| Submission date |
Aug 25, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Robert Lowe |
| Organization name |
QMUL
|
| Department |
Blizard Institute
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| Street address |
4 Newark Street
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| City |
London |
| ZIP/Postal code |
E1 2AT |
| Country |
United Kingdom |
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| Platform ID |
GPL22370 |
| Series (2) |
| GSE86058 |
The rate of ageing-associated DNA methylation dynamics is a molecular readout of lifespan variation amongst mammalian species [Bis-PCR: dog] |
| GSE86059 |
The rate of ageing-associated DNA methylation dynamics is a molecular readout of lifespan variation amongst mammalian species |
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| Relations |
| BioSample |
SAMN05660037 |
| SRA |
SRX2053540 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2292723.txt.gz |
12.2 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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