NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM6215255 Query DataSets for GSM6215255
Status Public on Dec 01, 2023
Title Tissue, Normal, No injection, N
Sample type SRA
 
Source name normal brain tissue
Organism Homo sapiens
Characteristics Sex: female
genotype: no
disease state: control
tissue: normal brain tissue
treatment: no
time: Day 0
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
 
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
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)
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
Relations
BioSample SAMN28898955
SRA SRX15623356

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

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap