|
| Status |
Public on Dec 22, 2021 |
| Title |
GR10 |
| Sample type |
SRA |
| |
|
| Source name |
blood
|
| Organism |
Canis lupus familiaris |
| Characteristics |
strain: German Shepherd
disease state: Canine forms of osteoarthritis
tissue: blood
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from RNAlater stored blood with the RiboPure™-Blood Kit (Ambion, Life Technologies, CA, USA).
From each sample 1 ug of high quality RNA (RNA integrity number (RIN) > 8) was used for non-stranded, paired-end cDNA library preparation (NEBNext Ultra II RNA Library Prep, Illumina).
Multiplexed total cDNA libraries were sequenced on one lane using the NovaSeq 6000 instrument with 2x150 bp paired-end sequencing cycles.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
The NovaSeq Xp output files with base calls and qualities were converted into FASTQ file format and demultiplexed. Sequence reads were trimmed using fastp program v0.12.5.
Quality of sequencing data was checked and combined in one FASTQ file using FastQC v0.11.7.
All reads that passed quality control were mapped to the dog reference genome CanFam3.1 and the NCBI annotation release 105 with HISAT2 aligner v2.1.0.
The read abundance was calculated using the featureCounts algorithm as part of the Subread package v2.0.1.
DESeq2 package was used to read the featureCounts data. The count data were subjected to a regularized-logarithm transformation. DESeq2 v1.26.0 to assess differential expression between groups. DESeq2 applies a generalized linear model (GLM) to count data assuming a negative binomial distribution.
Genome_build: dog reference genome CanFam3.1
Supplementary_files_format_and_content: CVS file with a matrix table with normalized gene counts for every gene and every sample.
|
| |
|
| Submission date |
Dec 20, 2021 |
| Last update date |
Dec 22, 2021 |
| Contact name |
Guillermo Giovambattista |
| E-mail(s) |
guillermogiovambattista@gmail.com
|
| Phone |
02214211799
|
| Organization name |
CONICET-UNLP
|
| Department |
Facultad de Ciencias Veterinarias
|
| Lab |
IGEVET
|
| Street address |
Calle 60 y 118 S/N
|
| City |
La Plata |
| State/province |
Buenos Aires |
| ZIP/Postal code |
1900 |
| Country |
Argentina |
| |
|
| Platform ID |
GPL25760 |
| Series (1) |
| GSE191273 |
Transcriptomic profile of peripheral blood reveals potential genetic biomarkers for diagnosis of Osteoarthritis in German shepherd dogs |
|
| Relations |
| BioSample |
SAMN24247267 |
| SRA |
SRX13456248 |
