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| Status |
Public on Mar 31, 2020 |
| Title |
Sample10_0hr_BL_1 |
| Sample type |
SRA |
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| Source name |
whole cord blood
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| Organism |
Homo sapiens |
| Characteristics |
storage time: 0hr
subject id: 1
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA from whole blood was extracted using a QIAamp DNA Blood Mini Kit (Qiagen: Cat. #51104). For DNA extraction from dried blood spots, one half of a single blood spot 79 was cut into small pieces and incubated with lysis buffer (1218μL) and Proteinase K (33μL) using Gensolve reagents (GenTegra: GVR-113) in an Incubator/vortex shaker set at 1400rpm for 90min, at 56°C (ThermoMixer® C, Eppendorf). The lysate was processed using a QIAamp DNA Blood Mini Kit (Qiagen: Cat. #51104).
RRBS libraries were generated from 100ng of high-quality dsDNA using the RRBS Methyl_seq System 1-16 (Ovation: Part #0353) and EpiTect Fast DNA Bisulfite kit (Qiagen: Cat. #59824) following the manufacturer’s protocols.
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
Reduced Representation |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
blood_card_counts_fdr.txt.gz
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| Data processing |
Adaptor sequences were trimmed using Trim Galore.
Additional filtering was performed to remove reads that did not contain an MspI site signature at the 5’ end using a script provided by NuGEN (https://github.com/nugentechnologies/NuMetRRBS/blob/master/ trimRRBSdiversityAdaptCustomers.py).
The reads were then aligned using Bismark (version 0.16.0) and sorted by Samtools (version 1.7).
We then used MethPipe (version 3.4.2) to identify significant differentially methylated CpG sites (DMCs) with at least 30X reads with FDR ≤ 0.05.
CompEpitool was used to annotate the differentially methylated CpG sites to the human genome (hg38).
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text files with at least 30X reads (formatted as "chr", "loc", "strand", "fdr", )
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| Submission date |
Mar 05, 2020 |
| Last update date |
Mar 31, 2020 |
| Contact name |
Stephen Matthews |
| Organization name |
University of Toronto
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| Street address |
1 King's College Circle
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| City |
Toronto |
| State/province |
Ontario |
| ZIP/Postal code |
M5S1A8 |
| Country |
Canada |
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| Platform ID |
GPL18573 |
| Series (1) |
| GSE146468 |
Impact of ex-vivo sample handling on DNA methylation profiles in human cord blood and neonatal dried blood spots |
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| Relations |
| BioSample |
SAMN14307366 |
| SRA |
SRX7857080 |
| 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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