characteristics.text: 2013-04-18T17:03:35Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2013-03-21T09:56:41Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA1877883
characteristics.characteristic: External Id
characteristics.text: Crop Genetics and Biotechnology, Dept. of Molecular Biology and Genetics, Aarhus University, Denmark
characteristics.characteristic: INSDC center name
characteristics.text: 2013-04-18T17:03:35Z
characteristics.characteristic: INSDC first public
characteristics.text: 2013-03-21T09:56:41Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS224979
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-1556:Lolium perenne, ecotype Falster
characteristics.characteristic: Submitter Id
characteristics.text: ArrayExpress
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0009737
characteristics.characteristic: broker name
characteristics.text: Protocols: Plants from Lolium perenne ecotype Falster were grown in the greenhouse for 75 days after cloning, and were subsequently transferred to the climate chamber for 58 days under simulated fall conditions (15C and 8 hours day length). A vernalization treatment was carried out for 9 weeks, at a temperature of 6C and 8 hours day length. Leaf material was collected before the start of vernalization, after 2 days, 4 weeks, and 9 weeks of vernalization, between 9-10 am. Total RNA was extracted using the RNeasy Plant Mini kit (Qiagen) following the manufacturers protocol. The RNA quality and concentration were assessed with the Agilent RNA 6000 Nano kit on the Agilent 2100 Bioanalyzer (Agilent Technologies). 10 ug of total RNA from each sample, representing material pooled from four individual plants, were used for the mRNA-Seq library construction, combining the protocol supplied with the mRNA-Seq Sample Prep Kit (Illumina, protocol version 1004898 Rev. D, September 2009) and the Multiplexing Sample Preparation Oliogonucleotide Kit. Poly-A containing mRNA was purified using poly-T oligonucleotide-attached magnetic beads and fragmented using divalent cations under elevated temperature. The RNA fragments were then copied into first strand cDNA using reverse transcriptase and random hexamer primers, followed by second strand cDNA synthesis using DNA Polymerase I and RNaseH. The short cDNA fragments were end-repaired using T4 DNA polymerase and Klenow DNA polymerase and a single A base were added to the cDNA fragments by using 3prime to 5prime exo-nuclease. This was followed by ligation of Illumina adaptors from the Multiplexing Sample Preparation Oliogonucleotide Kit and by gel purification of fragments of approximately 200 bp in size. The libraries were finally duplexed (index #6: GCCAAT or index #12: CTTGTA) and enriched by PCR for 18 cycles using the primers from the Multiplexing Sample Preparation Oliogonucleotide Kit. The index is a unique 6 bp sequence which is sequenced in a separate read, after sequencing the insert. The concentrations of the libraries were determined using a Qubit fluorometer (Invitrogen), and the size and purity of the libraries were determined with the Agilent 2100 Bioanalyzer in combination with the Agilent DNA 1000 Kit.
characteristics.characteristic: description
characteristics.text: Lolium perenne
characteristics.characteristic: organism
characteristics.text: Lolium perenne
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/NCBITaxon_4522
characteristics.characteristic: organism
characteristics.text: leaf
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/PO_0025034
characteristics.characteristic: organism part
characteristics.text: Lolium perenne
characteristics.characteristic: scientific_name
characteristics.text: frozen specimen
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/OBI_0000922
characteristics.characteristic: specimen with known storage state
characteristics.text: Falster
characteristics.characteristic: strain
characteristics.text: Lolium perenne, ecotype Falster
characteristics.characteristic: title