|
| Status |
Public on Sep 01, 2019 |
| Title |
F3 [Liver-NP0-3] |
| Sample type |
SRA |
| |
|
| Source name |
Liver
|
| Organism |
Anguilla anguilla |
| Characteristics |
tissue: Liver
contamination level: NP0
individual: Eel_3
|
| Extracted molecule |
total RNA |
| Extraction protocol |
SV Total RNA isolation system kit (Promega) according to manufacturer’s instructions
TruSeq RNA Library Prep Kit v2
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
F3
|
| Data processing |
Reads have been aligned to contigs with bwa (version 0.7.12) with standard parameters. Resulting sam files were sorted and indexed with samtools (version 1.1) with standard parameters. Expression counts were generated from the bam files with samtools.
Filtered reads were assembled using DRAP version 1.7 and the Trinity assembler (www.sigenae.org/drap)
Genome_build: Aanguilla_assembly.fasta
Supplementary_files_format_and_content: Aanguilla_raw counts : comma-separated csv file including count values for each sample
Supplementary_files_format_and_content: Aanguilla_assembly : fasta file listing the de novo assembled contigs
|
| |
|
| Submission date |
Feb 01, 2018 |
| Last update date |
Sep 01, 2019 |
| Contact name |
Fanny Perrier |
| Organization name |
Université de Bordeaux
|
| Street address |
place Peyneau
|
| City |
Arcachon |
| ZIP/Postal code |
33120 |
| Country |
France |
| |
|
| Platform ID |
GPL24571 |
| Series (1) |
| GSE110011 |
Transcriptomic profiling responses in liver and brain tissues of European eels Anguilla anguilla after a gold nanoparticle trophic exposure |
|
| Relations |
| BioSample |
SAMN08452229 |
