|
| Status |
Public on Jul 25, 2018 |
| Title |
MR1 |
| Sample type |
SRA |
| |
|
| Source name |
Head-Kidney, mutant reassortant strain
|
| Organism |
Solea senegalensis |
| Characteristics |
experimental group: rSs160.03-247+270
tissue: Head-Kidney
infection: Betanodaviruses mutant reassortant strain
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Organs were removed, flash frozen on liquid nitrogen and then passed to -80 ºC. RNA was harvested combining Trizol reagent and Qiagen RNeasy mini kit.
Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 2 ug of total RNA for the construction of sequencing libraries.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Processed data file: MR_allgenes_edgeR.txt
Processed data file: MR_Normalized_counts_edgeR.txt
Processed data file: MR_DEgenes_edgeR.txt
|
| Data processing |
RNA-Seq was performed using the Illumina HiSeq™ 2000 platform. Stranded mRNA-Seq application was selected obtaining >40 million paired-ended (PE) reads per sample with 2 x 75 bp reads length.
Pre-processing of raw reads was performed using SeqtrimNEXT (v2.0.60).
For the mapping and assembly of pre-processed FASTQ reads, we used the script Bowtie2 (v2.2.9) using reference transcriptome (Solea senegalensis v.4.1 2014-01-23).
To convert SAM mapping results to reference sequence counts, the script sam2counts (v20131126) was used.
Bioconductor project tools (EdgeR, DESeq2, and limma) were used for the analysis and comprehension of high-throughput transcriptomic data.
Genome_build: Solea senegalensis v.4.1 2014-01-23 (SoleaDB: http://www.juntadeandalucia.es/agriculturaypesca/ifapa/soleadb_ifapa/assemblies/46?tab=inf)
Supplementary_files_format_and_content: *_edgeR.txt: Tab-delimited text files include abundance measurements.
|
| |
|
| Submission date |
Jul 25, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Alejandro Labella |
| E-mail(s) |
amlabella@uma.es
|
| Phone |
952137412
|
| Organization name |
University of Malaga
|
| Department |
Microbiology
|
| Street address |
Boulevard Louis Pasteur campus teatinos Faculty of Sciences
|
| City |
Malaga |
| State/province |
Malaga |
| ZIP/Postal code |
29071 |
| Country |
Spain |
| |
|
| Platform ID |
GPL23830 |
| Series (1) |
| GSE101877 |
Transcriptomic profiles of Senegalese sole in response to infection with different reassortant strains of betanodavirus |
|
| Relations |
| BioSample |
SAMN07414649 |
| SRA |
SRX3034940 |
