Overview
Analysis Namede novo Northern Red Oak Ozone Treatment Experiment
Transcriptome NameRed Oak Ozone
MethodTrinity
SourceNorthern Red Oak Ozone
Date performed2011-10-10
Number of Contigs45,857

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 Contigs 45,857
Number of Contigs > 2K 2,401
Number of Assembled Sequences 941,558
Number of Unassembled Sequences 157,704
Contig N50 1,927 bases
Number of Sequences per Contig 20
Contig Average Length 814

Download assembled data:

Contigs (fasta format)
Contigs (qual format)

Read Statistics

Raw data can be downloaded from the NCBI SRA.

Library Name Treatment Reads Avg. Length NCBI SRA
A Control 265,243 361 SRX858560
B 150ppb 300,929 374 SRX858561
C 225ppb 272,736 353 SRX858562
D 300ppb 260,354 361 SRX858563