|
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.
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|
|
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 |