NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM4386307 Query DataSets for GSM4386307
Status Public on Mar 31, 2020
Title Sample14_4hr_CD_2
Sample type SRA
 
Source name whole cord blood on dried blood spot
Organism Homo sapiens
Characteristics storage time: 4hr
subject id: 2
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.
 
Library strategy Bisulfite-Seq
Library source genomic
Library selection Reduced Representation
Instrument model Illumina NextSeq 500
 
Description blood_card_counts_fdr.txt.gz
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", )
 
Submission date Mar 05, 2020
Last update date Mar 31, 2020
Contact name Stephen Matthews
Organization name University of Toronto
Street address 1 King's College Circle
City Toronto
State/province Ontario
ZIP/Postal code M5S1A8
Country Canada
 
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
Relations
BioSample SAMN14307362
SRA SRX7857084

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap