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Sample GSM6215257 Query DataSets for GSM6215257
Status Public on Dec 01, 2023
Title Tissue, Glioblastoma, First injection, T3 (day 70)
Sample type SRA
Source name tumor tissue
Organism Homo sapiens
Characteristics Sex: female
genotype: H3K27M mutant, IV
disease state: Glioblastoma
tissue: tumor tissue
treatment: oncolytic virus, first injection
time: Day 70
Extracted molecule total RNA
Extraction protocol Briefly, total RNA was used for removing the rRNAs with NEBNext rRNA Depletion Kit (New England Biolabs, Inc., Massachusetts, USA) following the manufacturer's instructions. RNA libraries were constructed by using NEBNext® Ultra™ II Directional RNA Library Prep Kit (New England Biolabs, Inc., Massachusetts,USA) according to the manufacturer’s instructions.
Libraries were controlled for quality and quantified using the BioAnalyzer 2100 system (Agilent Technologies, Inc., USA). Library sequencing was performed on an illumina NovaSeq 6000 instrument with 150bp paired end reads.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
Description Tumor tissue samples were collected before the two surgical injections of the oncolytic virus, so there were only uninjected tissue sample and tissue sample before the second injection. In other words, no tumor tissue samples were collected for mRNA sequencing after the second injection of the oncolytic virus.
Data processing Paired-end reads were harvested from Illumina NovaSeq 6000 sequencer, and were quality controlled by Q30
After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3), the high quality clean reads were aligned to the human reference genome (HG19) with hisat2 software (v2.0.4).
Then, HTSeq software (v0.9.1) was used to get the raw count, and edgeR was used to perform normalization, then differentially expressed mRNAs were identified by p-value and fold change.
Assembly: hg19
Supplementary files format and content: Excel format, raw counts, normalized counts
Submission date Jun 07, 2022
Last update date Dec 01, 2023
Contact name Lixin Ma
Organization name Sanbo Brain Hospital
Department Neurosurgery
Street address Haidian District
City Beijing
ZIP/Postal code 100093
Country China
Platform ID GPL24676
Series (2)
GSE205590 Genome-wide analysis of circulating tumor DNA methylation profiles in cerebrospinal fluid: a clinical trial of oncolytic virus for glioblastoma [mRNA-Seq]
GSE205591 Genome-wide analysis of circulating tumor DNA methylation profiles in cerebrospinal fluid: a clinical trial of oncolytic virus for glioblastoma
BioSample SAMN28898953
SRA SRX15623358

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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