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Sample GSM1358518 Query DataSets for GSM1358518
Status Public on Jul 01, 2014
Title C07
Sample type SRA
Source name whole blood
Organism Homo sapiens
Characteristics ethnicity: Not Hispanic
tissue: whole blood
gender: Female
race: White
Extracted molecule genomic DNA
Extraction protocol DNA extracted from whole blood and bisulfite treated with Qiagen EpiTect bisulfite conversion kits
Qiagen EpiTect bisulfite conversion kits
Library strategy Bisulfite-Seq
Library source genomic
Library selection RANDOM
Instrument model 454 GS FLX
Description Pooled sequences from 10 bisulfite PCR amplicon amplicons
Data processing fastq conversion, sff_extract 0.2.13, sff_to_fastq -Q -C
filter reads,FASTX Toolkit, fastx_clipper -l 100 -Q33
align to amplicon sequences, Bismark v0.7.7, bismark —fastq —bowtie2 —non_directional -N 1 -L 15 -D 20 -R 4
call SNPs, samtools 0.1.19-44428cd, samtools mpileup -D -E -Q 10 -u | bcftools view -Ig
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited, content describes genotype (0=homozygous alternate allele, 1=heterozygous, 2=homozygous reference allele) and information about SNP and CpG features including amplicon examined, feature ID (CpGID used in publication or SNP rsID), chromosomal location and SNP allele (0=alternate, 1=reference) or CpG methylation status (0=unmethylated, 1=methylated) for individual reads)CpG methylation calls for all reads
Submission date Mar 27, 2014
Last update date May 15, 2019
Contact name John N Hutchinson
Organization name Harvard Chan School of Public Health
Street address 677 Huntington Avenue
City Boston
State/province Massachusetts
ZIP/Postal code 02215
Country USA
Platform ID GPL9186
Series (1)
GSE56298 Allele-Specific Methylation Occurs at Genetic Variants Associated with Complex Disease
BioSample SAMN02709747
SRA SRX502435

Supplementary file Size Download File type/resource 17.1 Kb (ftp)(http) TAB
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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