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Sample GSM6214069 Query DataSets for GSM6214069
Status Public on Dec 01, 2023
Title Cerebrospinal fluid, Glioblastoma, Second injection, G4 (day 1)
Sample type SRA
 
Source name cerebrospinal fluid
Organism Homo sapiens
Characteristics disease state: glioblastoma
Sex: female
genotype: H3K27M mutant, IV
tissue: cerebrospinal fluid
treatment: oncolytic virus, second injection
time: Day 71
molecule type: ctDNA
ip antibody: monoclonal antibody against 5-methylcytosine
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was isolated using phenol–chloroform, precipitated with ethanol and sonicated to 100–500 bp using Bioruptor (Diagenode). Sonicated DNA was end repaired, A tailed, and ligated to adapters by using NEBNext® Ultra™ DNA Library Prep Kit (NEB). Then, MeDIP was performed with a monoclonal antibody against 5-methylcytosine by following the standard manufacturer’s protocol (Active Motif).
MeDIP DNA libraries were quantified using Quant-iT PicoGreen dsDNA Kits (Life Technologies), and subjected to high-throughput 150 base paired-end sequencing on Illumina Hiseq sequencer according to the manufacturer’s recommended protocol.
 
Library strategy MeDIP-Seq
Library source genomic
Library selection 5-methylcytidine antibody
Instrument model Illumina NovaSeq 6000
 
Data processing Briefly,  raw data were generated after sequencing,  image analysis, base calling and quality filtering on Illumina NovaSeq 6000 sequencer.
Q30 was used to perform quality control. After adaptor-trimming and low quality reads removing by cutadapt (v1.9.3) software, high quality clean reads were generated. Then these clean reads were aligned to Human reference genome  (HG19) using bowtie2  software  (v2.2.4) with default parameters.
Peak calling was performed with MACS software (v2.0). Differentially methylated regions were identified by diffReps software (v1.55.4).The methylated regions were then annotated with the latest UCSC RefSeq database to connect the peak information with the gene annotation.
Assembly: hg19
Supplementary files format and content: excel format
 
Submission date Jun 06, 2022
Last update date Dec 01, 2023
Contact name Lixin Ma
E-mail(s) dl01030517@126.com
Organization name Sanbo Brain Hospital
Department Neurosurgery
Street address Haidian District
City Beijing
ZIP/Postal code 100093
Country China
 
Platform ID GPL24676
Series (2)
GSE205519 Genome-wide analysis of circulating tumor DNA methylation profiles in cerebrospinal fluid: a clinical trial of oncolytic virus for glioblastoma [MeDIP-Seq]
GSE205591 Genome-wide analysis of circulating tumor DNA methylation profiles in cerebrospinal fluid: a clinical trial of oncolytic virus for glioblastoma
Relations
BioSample SAMN28870819
SRA SRX15597491

Supplementary file Size Download File type/resource
GSM6214069_G4.IP_vs_G1.Input.xlsx 2.1 Mb (ftp)(http) XLSX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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