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| Status |
Public on Jan 07, 2020 |
| Title |
1333.4 Sample 2 |
| Sample type |
SRA |
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| Source name |
placenta
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| Organism |
Callithrix jacchus |
| Characteristics |
maternal weight day 60: 347
maternal weight day 90: 391
maternal weight day 120: 439
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
genomic DNA was extracted using qiagen DNAeasy Blood and Tissue Kit
RRBS uses MspI which is a methylation insensitive restriction enzyme that recognizes CCGG sites. As MspI is insensitive to methylation status, all CCGG sites were cut between the two C's resulting in small fragments with a high frequency of potential CpG methylation sites. Following MspI digestion, the fragments underwent adaptor ligation, final repair, bisulfite conversion, and PCR amplification to produce the final libraries for sequencing. The 5 pools were sequenced on 5 lanes in the HiSeq 4000 (Illumina, San Diego, CA) with paired-end reads 100nt in length
RRBS Methyl-Seq System 1-16
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
Reduced Representation |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
Right; Disc 1
Z2099
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| Data processing |
low quality bases and adaptor sequences were trimmed
sequences were aligned to the marmoset genome using the bwa-meth R package
methylation status was determined using PileOMeth R pacakges
Genome_build: C_jacchus 3.2.1, verson 85 (GCA_000004665.1)
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| Submission date |
Jan 06, 2020 |
| Last update date |
Jan 07, 2020 |
| Contact name |
Derek Wildman |
| Organization name |
University of South Florida
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| Street address |
3720 Spectrum Blvd
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| City |
Tampa |
| State/province |
FL |
| ZIP/Postal code |
33612 |
| Country |
USA |
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| Platform ID |
GPL26566 |
| Series (1) |
| GSE143200 |
Maternal weight affects placental DNA methylation of genes invovled in metabolic pathways in the common marmoset monkey (Callithrix jacchus) |
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| Relations |
| BioSample |
SAMN13740807 |
| SRA |
SRX7508433 |
| 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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