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Sample GSM3076198 Query DataSets for GSM3076198
Status Public on Aug 07, 2019
Title blood_6
Sample type SRA
 
Source name Plasma
Organism Homo sapiens
Characteristics tissue: plasma
training/validation group: Training
Extracted molecule genomic DNA
Extraction protocol Plasma were separated from blood,then cfDNA were extracted from plasma using zymo research Quick-cfRNA Serum & Plasma, 10ng cfDNA was used for library construction.
DNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy MeDIP-Seq
Library source genomic
Library selection 5-methylcytidine antibody
Instrument model Illumina NextSeq 500
 
Data processing Bcl2fastq v2.17 software used to change the bcl files to fastq files.
Sequenced reads were trimmed for adaptor sequence using software trimmomatic v0.36, and masked for low-complexity or low-quality sequence, then mapped to hg19 genome using bowtie v2.26
Duplicate reads were marked using picard v1.141. The reads were counted for overlap with gene bodies (annotated by the GENCODE Project) using featureCounts v1.5.0-p3.
Genome_build: hg19
Supplementary_files_format_and_content: txt file for each sample with raw reads count summarised to genebody region.
 
Submission date Apr 04, 2018
Last update date Jun 05, 2023
Contact name Zhou Zhang
E-mail(s) zhou.zhang@northwestern.edu
Organization name Northwestern University
Department Preventive Medicine
Street address 680 North Lake Shore Drive, Suite 1400
City Chicago
State/province IL
ZIP/Postal code 60611
Country USA
 
Platform ID GPL18573
Series (1)
GSE112679 Genome-wide Mapping of 5-Hydroxymethylcytosines in Circulating Cell-free DNA as a Non-invasive Approach for Early Detection of Hepatocellular Carcinoma
Relations
BioSample SAMN08869473
SRA SRX3890007

Supplementary file Size Download File type/resource
GSM3076198_Seq_6.genebody.txt.gz 98.1 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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