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| Status |
Public on Mar 21, 2016 |
| Title |
7764_methyl-seq_T cell |
| Sample type |
SRA |
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| Source name |
T cell
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| Organism |
Homo sapiens |
| Characteristics |
tissue: T cell
diagnosis: normal
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA (500 ng) was extracted using Phenol-chloroform extraction protocol and bisulfite-converted using EZ DNA methylation kit (Zymo)
Target enrichment and libraries were prepared according to Agilent's instructions accompanying SureSelectXT Methyl-Seq Target Enrichment System for Illumina Multiplexed Sequencing kit.
Targeted bisulfite converted libraries, covering 84Mb and 3.7 million CpGs, using SureSelectXT Methyl-Seq Target Enrichment System for Illumina Multiplexed Sequencing.
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
Bisulfite converted DNA
Targeted methyl-seq library
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| Data processing |
Basecalls was performed using illumina CASAVA
Trimming of adaptors, low quality base calls (quality score <30), and exclusion of short reads (<40 bp) using TrimGalore
Alignment against human reference genome GRCh37 was performed using Bismark Aligner
Read deduplication was performed using Samtools
Methylation calling was performed using Bismark Methyl Extractor
CpGs with less than 10X coverage were filtered out
SNP calling was performed using BisSNP. SNPs with less than 10X per allele, as well as C>T SNPs on negative strand were excluded, since >95% of the enriched DNA aligned to the negative strand.
ASM calling was performed with Bismark, after separating the valid SNP-containing reads by allele.
Genome_build: GRCh37
Supplementary_files_format_and_content: The methylation percentage bedgraph files were generated using Bismark Methyl Extractor outputs, the values represent the percentage of methylation, CpGs with less than 10X coverage were filtered out; the vcf files contains the heterozygous SNPs called by BisSNP including their coordinates, reference and alternate alleles, as well the coverage for each allele.
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| Submission date |
Mar 11, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Benjamin Tycko |
| E-mail(s) |
bejamintycko@hackensackmeridian.org
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| Phone |
5519963595
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| Organization name |
HUMC
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| Department |
Epigenetics
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| Street address |
40 prospect avenue
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| City |
hackensack |
| State/province |
NJ |
| ZIP/Postal code |
07601 |
| Country |
USA |
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| Platform ID |
GPL11154 |
| Series (2) |
| GSE79148 |
Mechanisms and disease associations of haplotype-dependent allele specific DNA methylation: Methyl-seq data for the identification of hap-ASM |
| GSE79262 |
Mechanisms and disease associations of haplotype-dependent allele specific DNA methylation |
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| Relations |
| BioSample |
SAMN04549495 |
| SRA |
SRX1630670 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2087015_7764.vcf.gz |
233.6 Kb |
(ftp)(http) |
VCF |
| GSM2087015_7764_percentage.bedgraph.gz |
16.2 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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