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Sample GSM4182695 Query DataSets for GSM4182695
Status Public on Mar 24, 2020
Title Discovery_ASD_F_04
Sample type SRA
 
Source name umbilical cord blood
Organism Homo sapiens
Characteristics sample set: Discovery
tissue: umbilical cord blood
diagnosis: ASD
Sex: F
study: EARLI
Extracted molecule genomic DNA
Extraction protocol DNA was extracted from whole umbilical cord blood using the Gentra Puregene Blood Kit (Qiagen).
DNA was bisulfite converted with the EZ DNA Methylation Lightning kit (Zymo). WGBS libraries were prepared from 100ng of bisulfite-converted DNA using the TruSeq DNA Methylation kit (Illumina) with indexed PCR primers and a 14-cycle PCR program.
 
Library strategy Bisulfite-Seq
Library source genomic
Library selection RANDOM
Instrument model HiSeq X Ten
 
Description JLCM023B
Data processing Filtered raw fastq files using Illumina quality flag
Followed CpG_Me workflow v1.0 which included the steps below.
Trimmed to remove adapters and 5' and 3' methylation bias with Trim Galore! v0.4.5
Aligned to hg38 reference genome with Bismark v0.19.1
Removed PCR duplicates with Bismark v0.19.1
Extracted CpG methylation counts at all covered sites to generate genome-wide cytosine methylation reports with Bismark v0.19.1
Genome_build: hg38
Supplementary_files_format_and_content: Bismark genome-wide cytosine methylation report for each sample with columns for chromosome, CpG position, strand, methylated count, unmethylated count, dinucleotide context, and trinucleotide context
 
Submission date Nov 20, 2019
Last update date Mar 24, 2020
Contact name Charles E Mordaunt
E-mail(s) mordauntcharles@gmail.com
Organization name University of California, Davis
Department Medical Microbiology and Immunology
Lab LaSalle Lab
Street address 3318 Tupper Hall, One Shields Ave
City Davis
State/province CA
ZIP/Postal code 95616
Country USA
 
Platform ID GPL20795
Series (1)
GSE140730 Cord blood DNA methylome in newborns later diagnosed with autism spectrum disorder reflects early dysregulation of neurodevelopmental and X-linked genes
Relations
BioSample SAMN13337221
SRA SRX7191676

Supplementary file Size Download File type/resource
GSM4182695_JLCM023B_CpG_report.txt.gz 266.5 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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