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(Hybrid Transcriptome)
(Hybrid Transcriptome)
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To test this hypothesis, we sequenced the transcriptome of incompatible Col-0 X A. arenosa and partially compatible C24 X A. arenosa. We demonstrate that while release of gene suppression is evident for endosperm transcription factors, photosynthetic gene clusters, and ribosomal proteins, there is no early loss of transposable element regulation.
 
To test this hypothesis, we sequenced the transcriptome of incompatible Col-0 X A. arenosa and partially compatible C24 X A. arenosa. We demonstrate that while release of gene suppression is evident for endosperm transcription factors, photosynthetic gene clusters, and ribosomal proteins, there is no early loss of transposable element regulation.
  
This page is dedicated to resources that were used to assess gene expression (Sam Gene Counter script) and perform transposable element analysis.
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This page is dedicated to resources that were used to assess gene expression ([[Media:SamGeneCounter.zip |Sam Gene Counter script]]) and perform transposable element analysis.
  
  
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This[[Media:TAIR10_genes_TE_distance.txt.zip  | file]] is a table of the distance of Arabidopsis thaliana genes to the nearest transposable element.  
 
This[[Media:TAIR10_genes_TE_distance.txt.zip  | file]] is a table of the distance of Arabidopsis thaliana genes to the nearest transposable element.  
  
===Sam Gene Counter ===
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<!--===Sam Gene Counter ===
This [[Media:SamGeneCounter.zip | script]] generates a table with the number of reads from a sam file that aligned uniquely to a particular gene.
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This [[Media:SamGeneCounter.zip | script]] generates a table with the number of reads from a sam file that aligned uniquely to a particular gene.-->

Revision as of 16:26, 28 May 2013


Hybrid Transcriptome

Overview

When A. thaliana is crossed to close relative A. arenosa, a significant portion of seeds arrest during early seed development. We hypothesize that non-additive gene regulation is responsible for hybrid seed failure. To test this hypothesis, we sequenced the transcriptome of incompatible Col-0 X A. arenosa and partially compatible C24 X A. arenosa. We demonstrate that while release of gene suppression is evident for endosperm transcription factors, photosynthetic gene clusters, and ribosomal proteins, there is no early loss of transposable element regulation.

This page is dedicated to resources that were used to assess gene expression (Sam Gene Counter script) and perform transposable element analysis.



TE Distance

This file is a table of the distance of Arabidopsis thaliana genes to the nearest transposable element.


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