Good vs bad quality cork: high-throughput sequence of phellogenic tis... - SRA

SRX363291: Good vs bad quality cork: high-throughput sequence of phellogenic tissue
1 LS454 (454 GS FLX Titanium) run: 675,086 spots, 373.3M bases, 811Mb downloads

Design: Biological sample Phellogenic tissue was collected from 10 mature cork oaks under cork production (estimated age 50-70 years) in Southern Portugal. The sample was taken at the time of cork harvest, in the period of end July-beginning August 2011, by scratching the inside of the plank (the so-called cork belly, corresponding to the torn out phellogen) immediately after the separation of the cork plank from the tree stem, and freezing in liquid nitrogen right after the collection. Five samples were taken from cork oaks producing good quality cork and five samples from trees with bad quality cork were retained for analysis. cDNA preparation The quality of total RNA was verified on Agilent 2100 Bioanalyzer with the RNA 6000 Pico Kit (agilent Technologies, Waldbronn, Germany) and the quantity assessed by fluorimetry with the Quant-iT RiboGreen RNA kit (Invitrogen, CA, USA). A fraction of 0.5-2 micrograms of each pool of total RNA was used as starting material for cDNA synthesis with the MINT cDNA synthesis kit (Evrogen, Moscow, Russia), a strategy based on the SMART double-stranded cDNA synthesis methodology with amplification of polyA mRNA molecules using a modified template-switching approach that allows the introduction of known adapter sequences to both ends of the first strand cDNA. The synthesis were also done with a modified oligodT containing a restriction site for Bsgl to eliminate these tails and, in that way, minimize the interference of a A homopolymers during the 454 sequencing run. Non-normalized cDNA was quantified by fluorescence and sequence in 454 GS FLX Titanium according to the standard manufacturer’s instructions (Roche-454 Life Sciences, Bradford, CT, USA) at Biocant (Cantanhede, Portugal).

Submitted by: BIOFIG- FCUL

Study: Quercus suber Transcriptome or Gene expression

PRJNA218509 • SRP030001 • All experiments • All runs

show Abstracthide Abstract

The present work establishes a comparison of phellogenic genes differentially expressed during the development of cork of good and bad quality making use of Roche 454-pyrosequencing.

Sample: Fellogenic tissue_BQC

SAMN02351107 • SRS489988 • All experiments • All runs

Organism: Quercus suber

Library:

Name: Bad quality cork

Instrument: 454 GS FLX Titanium

Strategy: RNA-Seq

Source: TRANSCRIPTOMIC

Selection: cDNA

Layout: SINGLE

Spot descriptor:

5 forward

Runs: 1 run, 675,086 spots, 373.3M bases, 811Mb

Run	# of Spots	# of Bases	Size	Published
SRR1009172	675,086	373.3M	811Mb	2014-03-13

ID:: 515728

SRA

Sequence Read Archive

Result Filters

Send to:

Supplemental Content

Related information

Recent activity