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| Status |
Public on Jul 01, 2014 |
| Title |
A04 |
| Sample type |
SRA |
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| Source name |
whole blood
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| Organism |
Homo sapiens |
| Characteristics |
ethnicity: Not Hispanic
tissue: whole blood
gender: Female
race: White
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| 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
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
454 GS FLX |
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| Description |
Pooled sequences from 10 bisulfite PCR amplicon amplicons
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| Data processing |
fastq conversion, sff_extract 0.2.13, sff_to_fastq -Q -C
filter reads,FASTX Toolkit 0.0.13.2, 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
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| Submission date |
Mar 27, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
John N Hutchinson |
| Organization name |
Harvard Chan School of Public Health
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| Street address |
677 Huntington Avenue
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| City |
Boston |
| State/province |
Massachusetts |
| ZIP/Postal code |
02215 |
| Country |
USA |
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| Platform ID |
GPL9186 |
| Series (1) |
| GSE56298 |
Allele-Specific Methylation Occurs at Genetic Variants Associated with Complex Disease |
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| Relations |
| BioSample |
SAMN02709718 |
| SRA |
SRX502409 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1358492_A04.tab.gz |
8.6 Kb |
(ftp)(http) |
TAB |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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