Summary
Resource Type
Gene Expression Profile
Expression Data

This analysis contains expression data for 78834 features across 31 biosamples.

Download all expression data associated with this analysis.

Name
Black Walnut Ozone Treatments
Program, Pipeline, Workflow or Method Name
HTSeq; RPKM
Program Version
n/a
Date Performed
Tuesday, July 8, 2014 - 21:00
Data Source
Source Name
: Juglans nigra 120313
Source Version
: 120313
Description
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:

The experimental design included 4 levels of ozone across 3 exposure lengths. Black walnut seedlings were randomly assigned to 12 experimental groups:

  • Seedlings exposed to normal atmosphere for 7 hours (control)
  • Seedlings exposed to 80 ppb of ozone for 7 hours
  • Seedlings exposed to 125 ppb of ozone for 7 hours
  • Seedlings exposed to 225 ppb of ozone for 7 hours
  • Seedlings exposed to normal atmosphere for 14 days (control)
  • Seedlings exposed to 80 ppb of ozone for 14 days
  • Seedlings exposed to 125 ppb of ozone for 14 days
  • Seedlings exposed to 225 ppb of ozone for 14 days
  • Seedlings exposed to normal atmosphere for 28 days (control)
  • Seedlings exposed to 80 ppb of ozone for 28 days
  • Seedlings exposed to 125 ppb of ozone for 28 days
  • Seedlings exposed to 225 ppb of ozone for 28 days

At the end of the exposure time, mRNA was isolated from the leaf tissue of seedlings. The RNA was barcoded, pooled and sequenced using the Illulmina platform, yielding paired end reads of 151 x 151 bases.

Read Statistics

Library Reads Bases
BW1 - 7 hrs, control 445,258 67,233,958
BW2 - 7 hrs, 80ppb 477,680 72,129,680
BW3 - 7 hrs, 125ppb 557,356 84,160,756
BW4 - 7 hrs, 225ppb 415,176 62,691,576
BW5 - 14 days, control 450,004 67,950,604
BW6 - 14 days, 80ppb 497,990 75,196,490
BW7 - 14 days, 125ppb 528,592 79,817,392
BW8 - 14 days, 225ppb 452,432 68,317,232
BW9 - 28 days, control 440,366 66,495,266
BW10 - 28 days, 80ppb 383,622 57,926,922
BW11 - 28 days, 125ppb 547,984 82,745,584
BW12 - 28 days, 250ppb 457,592 69,096,392

Sequenced reads were trimmed with Trimmomatic and assembled with Trinity.

Assembly Statistics

Number of Putative Transcripts 61,770
Number of Components 41,321
Putative Transcript N50 1,328bp
Putative Transcript Average Length 854

Download assembled data:

Putative Transcripts (fasta format)

Predicted ORFs (fasta format)

Biosamples
NameTissueTreatmentDescription
BW-M-20undamaged leavesnoneBlack Walnut-Sparrow-Mother tree
BW-M-22undamaged twigsnoneBlack Walnut-Sparrow-Mother tree
BW-D-23damaged twigsmechanical woundingBlack Walnut-Schlesser-Father tree
BW-D-22undamaged twigsnoneBlack Walnut-Schlesser-Father tree
BW-M-23damaged twigsmechanical woundingBlack Walnut-Sparrow-Mother tree
BW-OW-9leafcontrol chamber ozone 10ppb+ mecanical wounding on day 28Black Walnut-offspring of Sparrow and Schlesser two yr.old (6 pooled seedlings)
BW-OW-11leafozone exposure 125ppb for 29 day + mecanical wounding on day 28Black Walnut-offspring of Sparrow and Schlesser two yr.old (6 pooled seedlings)
BW-M-19dormant twigsnoneBlack Walnut-Sparrow-Mother tree
BW-OW-12leafozone exposure 225ppb for 29 day + mecanical wounding on day 28Black Walnut-offspring of Sparrow and Schlesser two yr.old (6 pooled seedlings)
BW-D-28catkins (male flowers- very mature)noneBlack Walnut-Schlesser-Father tree

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