Summary
Name
[Archived] Quercus rubra - Transcriptome Assembly - Ozone
Resource Type
Transcriptome Assembly
Organism
Ontology Browser
View Gene Ontology browser or KEGG Ontology browser for Quercus rubra
Data Source
Source Name
: Northern Red Oak Ozone
Date Performed
Sunday, October 9, 2011 - 21:00
Number of transcripts
45,857
Average Transcript Length
814
Program, Pipeline, Workflow or Method Name
Trinity
Program Version
n/a
Description and Download
Description: 
This project aims to elucidate the molecular response of hardwood tree seedlings to varying levels of ozone concentration. Ozone pollution places environmental stress on forest trees resulting in early leaf senescence and loss of photosynthetic capacity. Such environmental stress poses a major challenge for high productivity and quality. Data from other species: View the poster from the 2011 ASPB meeting with more information and conclusions: Ozone Stress Response in Northern Red Oak

Methods

Red oak seedlings were treated for 30 days at 150, 225 or 300 ppb ozone as well as a control with no added ozone. Sequence libraries were constructed from mRNA isolated from leaf tissue from the three treatment groups plus the control group. The RNA was barcoded, pooled and sequenced using the 454 platform. Sequenced reads were assembled with DNASTAR NGen. Data has been uploaded to NCBI (BioProject PRJNA273270).
  • sample 'A' = control (no ozone exposure)
  • sample 'B' = 150 ppb
  • sample 'C' = 225 ppb
  • sample 'D' = 300 ppb

Assembly Statistics

Number of Contigs45,857
Number of Contigs > 2K2,401
Number of Assembled Sequences941,558
Number of Unassembled Sequences157,704
Contig N501,927 bases
Number of Sequences per Contig20
Contig Average Length814
Download assembled data:
Contigs (fasta format)
Contigs (qual format)

Read Statistics

Raw data can be downloaded from the NCBI SRA.
Library NameTreatmentReadsAvg. LengthNCBI SRA
AControl265,243361SRX858560
B150ppb300,929374SRX858561
C225ppb272,736353SRX858562
D300ppb260,354361SRX858563
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