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Status |
Public on Oct 27, 2020 |
Title |
FFPE canine oligodendroglioma - dog no. 50416 |
Sample type |
SRA |
|
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Source name |
FFPE canine oligodendroglioma
|
Organism |
Canis lupus familiaris |
Characteristics |
tissue: Oligodendroglioma Grade III tissue status: FFPE breed: Boxer age of dog: 7
|
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.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
|
|
Description |
50416_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
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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 |
SAMN16553762 |
SRA |
SRX9364155 |