|
| Status |
Public on Jan 19, 2022 |
| Title |
T0_Horse15 |
| Sample type |
SRA |
| |
|
| Source name |
Tracheal wash
|
| Organism |
Equus caballus |
| Characteristics |
breed: Thoroughbred
cell type: Tracheal wash derived cells
treatment: rest
group: ~2 months at rest
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Fresh tracheal wash cells were isolated, and total RNA was harvested using Trizol-Qiagen reagents. Total RNA was processed using NEBNext Ultra Directional RNA Library Prep Kit by Novogene (Novogene Europe) to generate cDNA libraries
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Raw sequencing reads were processed to remove adaptors and poor-quality sequences (Q25 and below) using the Cutadapt program
Quality control of trimmed data was assessed using FASTQC and Multiqc
Kallisto (0.46.0.1) was ran on all samples, using as its index the complete set of 59,087 predicted transcripts for the EquCab3.0 genome
Genome_build: EquCab3.0 genome
Supplementary_files_format_and_content: Matrix table with gene counts for every gene and every sample
|
| |
|
| Submission date |
Jul 30, 2021 |
| Last update date |
Jan 19, 2022 |
| Contact name |
Anna Eleonora Karagianni |
| Organization name |
The Roslin Institute and the Royal Dick School of Veterinary Studies
|
| Department |
Veterinary Clinical Sciences
|
| Street address |
Easter Bush Campus
|
| City |
Edinburgh |
| ZIP/Postal code |
EH25 8RG |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL26749 |
| Series (1) |
| GSE181221 |
Training-associated alterations in equine respiratory immunity using RNAseq |
|
| Relations |
| BioSample |
SAMN20505981 |
| SRA |
SRX11612982 |
