|
| Status |
Public on Jul 20, 2017 |
| Title |
CMC with NNV-infected DLB-1 fish 2 |
| Sample type |
SRA |
| |
|
| Source name |
CMC with NNV-infected DLB-1 fish 2
|
| Organism |
Dicentrarchus labrax |
| Characteristics |
cell type: Head-kidney leucocytes
sample type: DLB-1 cell line infected with nodavirus
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from cells was isolated by PureLink® RNA Mini Kit
Libraries from the total RNA were prepared using the TruSeq®Stranded mRNA LT Sample Prep Kit from 0,5 µg of RNA
RNA-seq. Each library was sequenced using TruSeq SBS Kit v3-HS, in paired end mode with the read length 2x76bp
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Images analysis, base calling and quality scoring of the run were processed using the manufacturer’s software Real Time Analysis (RTA 1.13.48) and followed by generation of FASTQ sequence files by CASAVA 1.8
RNA-seq data were aligned to the Dicentrarchus labrax assembly with GEM v1.7
RNA-seq reads were re-aligned with the GEMtools RNA-seq pipeline v1.7
Differentially expressed genes (DEGs) were determined with the DESeq2 R package
Genome_build: Dicentrarchus labrax assembly with GEM v1.7
|
| |
|
| Submission date |
Jul 19, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
ALBERTO CUESTA |
| E-mail(s) |
[email protected]
|
| Phone |
+34 868 884536
|
| Organization name |
UNIVERSITY OF MURCIA
|
| Department |
CELL BIOLOGY AND HISTOLOGY
|
| Street address |
CAMPUS UNIVERSITARIO ESPINARDO, FACULTAD BIOLOGIA
|
| City |
MURCIA |
| State/province |
MURCIA |
| ZIP/Postal code |
30100 |
| Country |
Spain |
| |
|
| Platform ID |
GPL23808 |
| Series (1) |
| GSE101662 |
Cell-mediated cytotoxicity (CMC) in European sea bass leucocytes |
|
| Relations |
| BioSample |
SAMN07370993 |
| SRA |
SRX3021072 |
