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| Status |
Public on Aug 23, 2022 |
| Title |
100225599-cffDNA |
| Sample type |
SRA |
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| Source name |
cffDNA
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| Organism |
Macaca mulatta |
| Characteristics |
group: Restriction
timepoint: GD90
infantid: 3123107
birthgd: 157
c_section: No
foster: No
cohort: Year1
sample type: cffDNA
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Automated. Promega Maxwell RSC ccfDNA Plasma Kit for cffDNA and Tecan workflow for Zymo Quick-DNA Miniprep Plus Kit for brain.
Swift BioSciences Accel-NGS Methyl-Seq DNA Library Kit
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
The CpG_Me pipeline (https://github.com/ben-laufer/CpG_Me) was used to perform all data processing steps.
Trim Galore was used to trim adapters and methylation bias.
FastQ Screen was used to screen for sample contamination.
Bismark was used align to the reference genome, remove PCR duplicates, calculate coverage, extract CpG methylation, and generate genome-wide cytosine reports (CpG count matrices).
Picard Tools was used to calculate insert size metrics.
MultiQC was used for quality control.
Genome_build: rheMac10
Supplementary_files_format_and_content: Bismark genome-wide cytosine reports (CpG count matrices)
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| Submission date |
Mar 29, 2021 |
| Last update date |
Aug 23, 2022 |
| Contact name |
Benjamin I Laufer |
| Organization name |
Genentech
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| Street address |
1 DNA Way
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| City |
South San Francisco |
| State/province |
California |
| ZIP/Postal code |
94080 |
| Country |
USA |
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| Platform ID |
GPL27943 |
| Series (1) |
| GSE171064 |
Multi-omic brain and behavioral correlates of cell-free fetal DNA methylation in macaque maternal obesity models |
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| Relations |
| BioSample |
SAMN18527304 |
| SRA |
SRX10468706 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5218068_100225599-cffDNA_1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz.CpG_report.txt.gz |
240.4 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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