 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Aug 26, 2022 |
| Title |
MWMH00851_4_0 |
| Sample type |
SRA |
| |
|
| Source name |
Primary Tumor
|
| Organism |
Homo sapiens |
| Characteristics |
case id: MWMH00851
tissue: Primary Tumor
cell type: High Grade Serous Ovarian Cancer
survival group: LTS
survival group_lts: yes
library strand_orientation: reverse stranded
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from frozen tissue sections using either the miRNeasy Mini Kit (Qiagen), AllPrep DNA/RNA/miRNA Universal Kit (Qiagen), or mirVana miRNA Isolation Kit (Ambion/Life Technologies)
Quality assessment was performed using the Bioanalyzer RNA 6000 Nano assay (Agilent), finding a median RNA integrity number of 9.0 (range 4.7 to 10). Total RNA (1 ug) was used for library preparation using Illumina Stranded mRNA Prep and 150 bp paired-end sequencing was performed to a minimum of 100 million reads on Illumina NovaSeq 6000 instruments at the AGRF in accordance with the manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Raw data uploaded to European Genome-phenome Archive (EGA) repository under the accession code EGAD00001008537
|
| Data processing |
Initial QC on the raw FASTQ files were done using FastQC (v0.11.8)
Reads were trimmed for low quality, adapters, N content and poly-A tails using fastq-mcf (v1.05)
Contamination was checked using FastQ Screen (v0.11.4)
Reads were mapped to the human reference GRCh37.92 using the STAR two pass method (v2.6.0b)
Mapped reads were sorted using Picard Tools (v2.17.3)
Additional QC after mapping was performed using Picard Tools CollectRnaSeqMetrics (v2.17.3) and RSeQC (v 2.6.4)
Counts were generated on the ensemble release GRCh37.92 GTF annotation using HTSeq (v0.10.0). Counts were done on the exons only using the “intersection-nonempty” mode
Assembly: hg19
Supplementary files format and content: Raw counts, gene by sample matrix. The GeneID column is in the format "EnsemblID|Chromosome|Start|End|Strand|Whole_Gene_Length|Exon_Only_Length|Gene_Symbol|Gene_Biotype", eg.. "ENSG00000000003|X|99883667|99894988|-|11322|2968|TSPAN6|protein_coding"
Supplementary files format and content: TMM normalized log2 counts, gene by sample matrix. The raw counts were first filtered to only contain protein coding genes. Genes were further filtered to only contain genes with a CPM of > 0.5 in at least 10 samples. The data was then TMM normalized using edgeR (v3.28.1) and batch corrected for strand orientation differences (library_strand_orientation) while retaining comparison survival group differences (survival_group_LTS) by limma's (v3.42.2) removeBatchEffect function [i.e. limma::removeBatchEffect(log2_tmm_data, batch = library_strand_orientation, design = model.matrix(~survival_group_LTS))].
|
| |
|
| Submission date |
Aug 19, 2022 |
| Last update date |
Nov 08, 2022 |
| Contact name |
Dale W Garsed |
| E-mail(s) |
dale.garsed@petermac.org
|
| Organization name |
Peter MacCallum Cancer Centre
|
| Street address |
305 Grattan St
|
| City |
Melbourne |
| State/province |
VIC |
| ZIP/Postal code |
3000 |
| Country |
Australia |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE211669 |
The genomic and immune landscape of long-term survivors of high-grade serous ovarian cancer [RNAseq] |
| GSE211687 |
The genomic and immune landscape of long-term survivors of high-grade serous ovarian cancer |
|
| Supplementary data files not provided |
| Raw data not provided for this record |
| Processed data are available on Series record |
|
|
|
|
 |
