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Status |
Public on Dec 01, 2023 |
Title |
Tissue, Normal, No injection, N |
Sample type |
SRA |
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Source name |
normal brain tissue
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Organism |
Homo sapiens |
Characteristics |
Sex: female genotype: no disease state: control tissue: normal brain tissue treatment: no time: Day 0
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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.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
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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
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Submission date |
Jun 07, 2022 |
Last update date |
Dec 01, 2023 |
Contact name |
Lixin Ma |
E-mail(s) |
dl01030517@126.com
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Organization name |
Sanbo Brain Hospital
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Department |
Neurosurgery
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Street address |
Haidian District
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City |
Beijing |
ZIP/Postal code |
100093 |
Country |
China |
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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 |
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Relations |
BioSample |
SAMN28898955 |
SRA |
SRX15623356 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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