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| Status |
Public on Jun 05, 2014 |
| Title |
Muscle biospy sample 5 |
| Sample type |
SRA |
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| Source name |
Muscle
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| Organism |
Macaca fascicularis |
| Characteristics |
tissue: Muscle
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
5 µg genomic DNA was fragmented by sequential restriction enzyme digestion for 2 hrs each by 150 U each of MspI and TaqαI (Catalogue Nos.: R0106S and R0149M, New England Biolabs) at optimal temperatures, according to manufacturer’s instructions.
Illumina’s RRBS for Methylation Analysis protocol was followed, except that 10 µL of the methylation adapter oligo was used and the ligation was performed for 15 min at 20 °C in the adapter-ligation step. The purified fragments were then bisulphite treated using the EZ-96 DNA Methylation-Gold Kit (Catalogue No.: D5007, Zymo Research), according to manufacturer’s instructions.
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
Reduced Representation |
| Instrument model |
Illumina Genome Analyzer IIx |
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| Data processing |
Sequencing was performed on the Illumina Genome Analyzer IIx platform, as per manufacturer’s instructions.
Raw reads were filtered and trimmed (i.e. base quality < 20 were removed, read length < 20 bp were removed and entire read pair is removed if one of the trimmed reads become shorter than 20 bp), and then aligned against the Cynomolgus macaque genome (Yan et al., 2011) using RRBSMAP (Xi et al., 2012) with default settings (-p 8 -v 0.1 -w 100 -s 12 -D C-CGG).
We filtered for CpGs with at least 10x read coverage and estimated their methylation ratios using the python script methratio in RRBSMAP.
Genome_build: Cynomolgous macaque genome (BGI)
Supplementary_files_format_and_content: tab-delimited text files include methylation values for each Sample ...
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| Submission date |
Dec 23, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Joanna Holbrook |
| E-mail(s) |
joanna_holbrook@sics.a-star.edu.sg
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| Organization name |
SICS
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| Street address |
30 Medical Drive
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| City |
Singapore |
| ZIP/Postal code |
117609 |
| Country |
Singapore |
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| Platform ID |
GPL17720 |
| Series (2) |
| GSE53593 |
Infinium Monkeys: Infinium 450K array for the Cynomolgus macaque (Macaca fascicularis) RRBS-seq |
| GSE53596 |
Infinium Monkeys: Infinium 450K array for the Cynomolgus macaque (Macaca fascicularis) |
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| Relations |
| BioSample |
SAMN02485426 |
| SRA |
SRX398280 |
| 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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