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Sample GSM4074551 Query DataSets for GSM4074551
Status Public on Mar 18, 2020
Title sample_29_brain
Sample type SRA
 
Source name brain
Organism Homo sapiens
Characteristics subject id: SUB46
cancer status: non-cancer
organ: brain
Treatment protocol None
Growth protocol None
Extracted molecule genomic DNA
Extraction protocol DNA extracted using phenol-chloroform protocol after RNAse treatment. DNA was bisulfite converted with the EZ DNA methylation kit (Zymo).
Agilent SureSelect methyl-seq DNA hybrid capture kit was used according to the manufacturer’s instructions.
 
Library strategy Bisulfite-Seq
Library source genomic
Library selection RANDOM
Instrument model Illumina HiSeq 2500
 
Description SureSelect XT Methyl-Seq Target Enrichment System
Data processing Basecalls was performed using CASAVA
After trimming for low-quality bases (Phred score<30) and reads with a length <40 bp with TrimGalore, the reads were aligned to the human genome (GRCh37) using Bismark with paired end mode and default setting. Unpaired reads after trimming were aligned separately using single end-mode and the same settings.
Duplicate reads were removed using Picard tools.
SNP calling was performed with BisSNP [47] using default settings, except for the maximum coverage filter set at 200. C>T SNPs on negative strand were filtered out as well as heterozygous SNPs with less than 5 reads per allele. In addition, SNP with multiple mapping positions were filtered out, as well as SNPs with more than one minor allele with allele frequency>0.05. or deviating significantly from Hardy-Weinberg equilibrium based on exact tests corrected for multiple tests
ASM calling was performed after separating the SNP-containing reads by allele using R. After Bismark methylation extractor is applied, CpG methylation calls by allele are retrieved using allele tagged read IDs. Paired reads with ambiguous SNP calling (i.e., called as REF allele on one paired end and ALT allele on the other) were discarded.
Genome_build: GRCh37
Supplementary_files_format_and_content: Processed files per sample contain difference in methylation percentage at the CpG level between the alternate and reference alleles for each SNPs associated with high confidence ASM (observed in >2 biological samples) if the given sample was informative. The columns include chromosome, start and end of the CpG (reported on positive strand), difference in methylayion percentage and SNP ID. The unique identifier in these files is the CpG coordinate AND SNP ID.
 
Submission date Sep 11, 2019
Last update date Mar 20, 2020
Contact name Benjamin Tycko
E-mail(s) bejamintycko@hackensackmeridian.org
Phone 5519963595
Organization name HUMC
Department Epigenetics
Street address 40 prospect avenue
City hackensack
State/province NJ
ZIP/Postal code 07601
Country USA
 
Platform ID GPL16791
Series (2)
GSE137287 Genome-wide targeted methyl-seq: Allele-specific DNA methylation is increased in cancers and its dense mapping in normal plus neoplastic cells increases the yield of disease-associated regulatory SNPs I
GSE137880 Whole genome bisulfite sequencing and Genome-wide targeted methyl-seq: Allele-specific DNA methylation is increased in cancers and its dense mapping in normal plus neoplastic cells increases the yield of disease-associated regulatory SNPs
Relations
BioSample SAMN12730407
SRA SRX6831790

Supplementary file Size Download File type/resource
GSM4074551_9379_BRAIN_diff_cpg_level.txt.gz 28.6 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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