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| Status |
Public on Aug 24, 2020 |
| Title |
GBM.9 |
| Sample type |
SRA |
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| Source name |
Brain, Neurosurgical fluid, Extracellular Vesicles
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| Organism |
Homo sapiens |
| Characteristics |
disease state: Glioblastoma, Grade IV astrocytoma
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| Treatment protocol |
No treatment
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extraction by plasma/serum circulating and exosomal RNA purification kit (Slurry Format; Norgen Biotek Corp, ON, Canada; Cat No. 42800)
Starting total template CUSA-EV RNA (4 ng) was used to prepare the small RNA (sRNA) libraries using a QIASeqTM miRNA Library Kit (Qiagen, Venlo, Netherlands)
NGS was performed on an Illumina® NextSeqTM 500 NGS System (Illumina, San Diego, CA, USA). The libraries were sequenced in a single-end 75 bp, high-output protocol to generate an output of up to 400 million reads at a Q30 > 85 %
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| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
sncRNA data
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| Data processing |
The fastq files were uploaded to the Qiagen GeneGlobe® Data Analysis Centre for analysis by the QiaSeq® miRNA primary quantification pipeline (Qiagen, Venlo, Netherlands)
3’ adapter and low-quality bases were trimmed from the reads using Cutadapt
Insert sequences and unique molecular index (UMI) sequences were identified and annotated and Bowtie was used to remove known contaminants by sequentially aligning the reads
Reads were mapped by perfect match to miRBase mature, miRBase hairpin, noncoding RNA, mRNA and other RNA. At each step, only unmapped sequences passed to the next step and remaining unmapped sequences were mapped to the human miRBase mature database (human: Genome Reference Consortium GRCh38) where up to two mismatches were tolerated
Genome_build: Genome Reference Consortium GRCh38
Supplementary_files_format_and_content: .xlsx normalized read and UMI counts and differential expression data
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| Submission date |
Jun 01, 2020 |
| Last update date |
Aug 24, 2020 |
| Contact name |
Susannah Hallal |
| E-mail(s) |
susannah.hallal@lh.org.au
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| Organization name |
Chris O'Brien Lifehouse
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| Department |
Neurosurgery
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| Lab |
Neuropathology
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| Street address |
119-143 Missenden Road
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| City |
Sydney |
| State/province |
NSW |
| ZIP/Postal code |
2050 |
| Country |
Australia |
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| Platform ID |
GPL18573 |
| Series (1) |
| GSE151547 |
Deep sequencing of small RNAs from neurosurgical extracellular vesicles substantiate miR-486-3p as a circulating biomarker that distinguishes glioblastoma from lower-grade astrocytoma patients |
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| Relations |
| BioSample |
SAMN15074642 |
| SRA |
SRX8439926 |
| 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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