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Sample GSM4860374 Query DataSets for GSM4860374
Status Public on Oct 27, 2020
Title FFPE canine oligodendroglioma - dog no. 44331
Sample type SRA
 
Source name FFPE canine oligodendroglioma
Organism Canis lupus familiaris
Characteristics tissue: Oligodendroglioma Grade III
tissue status: FFPE
breed: French Bulldog
age of dog: 7.9
Treatment protocol All brain tissues samples during necropsy, and collection time varied from 1 to 18 hours after death. Samples were either frozen at -80 ° C (FF); or/and immersion-fixed in 10% neutral buffered formalin and paraffin-embedded fixation as tissue blocks.
Extracted molecule total RNA
Extraction protocol RNA extraction using the QIAGEN RNeasy® Mini Kit
The RNA-seq libraries were prepared using the Lexogen CORALL Total RNA-Seq Library Prep Kit which generates labelled with 12nt long Unique Molecular Identifiers (UMIs), forward stranded libraries for the transcriptome analyses. After the library preparation, the samples were amplified by PCR and finally purified to remove PCR components that could interfere with further RNA-seq quantification. Then, paired-end reads were generated by the Illumina NovaSeq 6000.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description 44331_FFPE_od
Data processing Trimming and removal of adapters was pwrformed using fastp tool. Due to the specificity of the CORALL Total RNA-Seq Library Prep Kit, 12nt long UMIs at the beginning 5’ of the forwarding read were also removed. The fastp tool was used with following options: --umi --umi_loc read1 --umi_len 12 --trim_poly_g --trim_poly_x --cut_by_quality3 --detect_adapter_for_pe --dont_overwrite -i input_read1.fastq.gz -I input_read2.fastq.gz -o trimmed_read1.fastq.gz -O trimmed_read2.fastq.gz
Before alignment, a STAR index was created using the full Canis lupus familiaris reference genome (Ensembl genome assembly: CanFam3.1 GCA_000002285.2) with "overhang" parameter set to 50: STAR --runThreadN 8 --runMode genomeGenerate --genomeDir ${indexDir}/ --genomeFastaFiles Canis_lupus_familiaris.CanFam3.1.dna.toplevel.fa --sjdbGTFfile Canis_lupus_familiaris.CanFam3.1.100.gtf --sjdbOverhang 50
Reads were aligned against the full Canis lupus familiaris reference genome (Ensembl genome assembly: CanFam3.1 GCA_000002285.2) using previously created STAR index. The STAR tool was set to the following options: STAR --genomeDir ${indexDir} --sjdbGTFfile ${ref} --sjdbOverhang 50 --outSAMtype BAM SortedByCoordinate --outSAMattributes NH HI NM MD AS nM jM jI XS --readFilesIn trimmed_read1.fastq.gz trimmed_read2.fastq.gz --readFilesCommand zcat
Using Ensembl Canis_lupus_familiaris.CanFam3.1.100.gtf annotation the reads were counted at gene level using featureCounts tool with following options: featureCounts -p -C -s 1 -T 1 -Q 10 -a ${ref} -t exon -g gene_id -o FCresult.txt ${folder_with_all_BAM_files}/*bam
Genome_build: CanFam3.1 GCA_000002285.2
Supplementary_files_format_and_content: FCresult.txt file with counts at gene level for all samples
 
Submission date Oct 26, 2020
Last update date Oct 27, 2020
Contact name Diana Solis
E-mail(s) diana.solis@unifr.ch
Phone +41795768779
Organization name The University of Bern
Department Vetsuisse Faculty
Street address Länggassstrasse 120
City Bern
ZIP/Postal code 3012
Country Switzerland
 
Platform ID GPL25760
Series (1)
GSE160124 Suitability of formalin-fixed paraffin-embedded tumor tissue for unbiased tumor-associated antigen identification
Relations
BioSample SAMN16553748
SRA SRX9364154

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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