|
| Status |
Public on Mar 21, 2024 |
| Title |
apocrine gland anal sac adenocarinoma (AGASAC), 2 [a2.1 RNA-seq] |
| Sample type |
SRA |
| |
|
| Source name |
archival FFPE tumour tissue
|
| Organism |
Canis lupus familiaris |
| Characteristics |
tissue: archival FFPE tumour tissue
animal: male, neutered
breed: Border Collie
dv200 (%): 73.5
age (years): 9
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted utilising the PureLinkTM FFPE Total RNA Isolation Kit (Thermo Fisher Scientific Inc., Waltham, MA, USA). After DNase I treatment 500 - 1000 ng total RNA was used for library construction.
QuantSeq 3' mRNA-Seq FWD Library Preparation Kit (Lexogen GmbH, Vienna, Austria) was used according to the manufacturer's guidelines (user guide 015UG009V0251) using the low-quality RNA protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
a2.1
|
| Data processing |
The FASTQ sequencing files were preprocessed (adapter trimmed, filtered) using Cutadapt and aligned to the NCBI Reference Sequence (RefSeq) assembly for the dog (Canis lupus familiaris) CanFam3.1 with the STAR aligner. Read counts per gene were generated with two rounds of featureCounts to mitigate the effect of too short 3' UTR annotations. Reads that remained unassigned in the first round were subjected to the second round of featureCounts on an adjusted annotation with a 3' extension by 2 kilobases. Differential gene expression analysis for the comparison apocrine gland anal sac adenocarcinoma (AGASAC) versus hepatoid gland adenoma (HGA) was performed with R using DESeq2. Significance thresholds were drawn at a log2(fold change) of ≤ -1 or ≥ 1 and an adjusted p-value of ≤ 0.05.
https://www.lexogen.com/wp-content/uploads/2019/03/015UG009V0251_QuantSeq_Illumina.pdf
Assembly: CanFam3.1 (NCBI RefSeq assembly: GCF_000002285.3)
Supplementary files format and content: tab-delimited text file including raw and normalised counts and differential gene expression data for each sample
|
| |
|
| Submission date |
Mar 18, 2024 |
| Last update date |
Mar 21, 2024 |
| Contact name |
Alexander F. H. Haake |
| E-mail(s) |
alexander.haake@fu-berlin.de
|
| Organization name |
Freie Universität Berlin
|
| Department |
Department of Veterinary Medicine
|
| Lab |
Institute of Veterinary Pathology
|
| Street address |
Robert-von-Ostertag-Straße 15
|
| City |
Berlin |
| ZIP/Postal code |
14163 |
| Country |
Germany |
| |
|
| Platform ID |
GPL21400 |
| Series (1) |
| GSE261790 |
Strong Correlation of Gene Counts and Differentially Expressed Genes between a 3′ RNA-Seq and RNA Hybridisation Platform from Canine Archival Tissue [3' RNA-Seq] |
|
| Relations |
| BioSample |
SAMN40517834 |
| SRA |
SRX23975662 |
