characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2014-02-01T17:00:46Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2018-03-08T16:42:11Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA2189179
characteristics.characteristic: External Id
characteristics.text: CNRS
characteristics.characteristic: INSDC center name
characteristics.text: 2014-02-01T17:00:46Z
characteristics.characteristic: INSDC first public
characteristics.text: 2018-03-08T16:42:11Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS348880
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-1867:brain_sample_2
characteristics.characteristic: Submitter Id
characteristics.text: ArrayExpress
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0009737
characteristics.characteristic: broker name
characteristics.text: European seabass
characteristics.characteristic: common name
characteristics.text: Protocols: Seabasses were sacrificed at midnight and midday. Brain and livers were collected and were stored in RNAlater (Invitrogen, Saint-Aubin, France) at 4C overnight. RNAlater was then removed and samples were stored at -80C until use. Total RNA from liver and brain was isolated using TRIzol (Invitrogen, Carlsbad, CA). Samples were treated with the DNA-free kit (Invitrogen, Saint-Aubin, France) using the manufacturers protocol. Total RNA was measured with a Nanodrop2000 (Thermo Scientific, Villebon-sur-Yvette, France). Total RNA pools of brain and liver were used for RNA-seq. Double stranded cDNA preparation and sequencing were performed at the BioPuces Strasbourg Department of the Institut de Genetique et de Biologie Moleculaire et Cellulaire (IGBMC Strasbourg, France). Sample preparation was performed using the Illumina mRNA sample preparation kit (Cat.No. RS-930-1001), involving the following steps. Poly-A containing mRNA were isolated from 4 ug of total RNA. The mRNA was then fragmented using divalent cations under elevated temperature (incubation time was reduced in order to obtain longer fragments). The cleaved RNA fragments were reverse transcribed into first stranded cDNA using random primers, second strand cDNA was then synthesized. Adaptors were ligated to the end-repaired cDNA. At the purification step, we selected two size ranges of templates: a pool of 350 and a pool of 500 base pair (bp) long. From then on, these two banks were treated separately for downstream enrichment by PCR and for paired-end RNA-seq. One flow cell was dedicated to each organ, and to each fragment size, i.e., a total of four flow cells (half a run) were employed.
characteristics.characteristic: description
characteristics.text: wild type genotype
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0005168
characteristics.characteristic: genotype
characteristics.text: Dicentrarchus labrax
characteristics.characteristic: organism
characteristics.text: Dicentrarchus labrax
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/NCBITaxon_13489
characteristics.characteristic: organism
characteristics.text: brain
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/UBERON_0000955
characteristics.characteristic: organism part
characteristics.text: Dicentrarchus labrax
characteristics.characteristic: scientific_name
characteristics.text: fresh specimen
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/OBI_0000971
characteristics.characteristic: specimen with known storage state
characteristics.text: brain_sample_2
characteristics.characteristic: title