|
| Status |
Public on Sep 20, 2017 |
| Title |
Individual 17 |
| Sample type |
SRA |
| |
|
| Source name |
upstream_2010
|
| Organism |
Margaritifera margaritifera |
| Characteristics |
location: upstream
year: 2010
age class: middle-aged
tissue: kidney
|
| 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 |
R70_CAGATC_L003
|
| 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: Margaritifera_assembly.fas
Supplementary_files_format_and_content: raw counts : comma-separated csv file including count values for each sample / assembly : fasta file
|
| |
|
| Submission date |
Feb 06, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Anthony Bertucci |
| Organization name |
University of Bordeaux
|
| Street address |
Place du Dr Peyneau
|
| City |
Arcachon |
| ZIP/Postal code |
33120 |
| Country |
France |
| |
|
| Platform ID |
GPL23031 |
| Series (1) |
| GSE94542 |
Transcriptomic responses of the endangered freshwater mussel Margaritifera margaritifera to trace metal contamination in the Dronne River, France |
|
| Relations |
| BioSample |
SAMN06299354 |
| SRA |
SRX2539391 |
