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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Early transcriptional changes in Medicago truncatula upon Nod factor treatment

ABSTRACT: This experiment was part of a larger study to elucidate the early effects of Nod factor treatment on the Medicago truncatula phosphoproteome, transcriptome and metabolome in wildtype and two mutants. In this experiment, RNA-Seq was used to measure transcriptional changes in plant roots treated +/- Nod factors for 1 hr. All plants were treated for one hour by replacement of the medium with modified Fahraeus medium with and without 10â8 molar Nod factors obtained from Sinorhizobium meliloti strain Rm1021 pRmE43 (pTE3:nodD1). Seedlings were harvested after one hour of treatment. RNA was extracted and sequenced from three biological replicates of each treatment condition in wildtype as well as mutants in nfp and dmi3, two genes known to be involved in the response pathway.

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Medicago truncatula

SUBMITTER: Michael Sussman

PROVIDER: E-MTAB-5064 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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A proteogenomic survey of the Medicago truncatula genome.

Volkening Jeremy D JD Bailey Derek J DJ Rose Christopher M CM Grimsrud Paul A PA Howes-Podoll Maegen M Venkateshwaran Muthusubramanian M Westphall Michael S MS Ané Jean-Michel JM Coon Joshua J JJ Sussman Michael R MR

Molecular & cellular proteomics : MCP 20120705 10

Peptide sequencing by computational assignment of tandem mass spectra to a database of putative protein sequences provides an independent approach to confirming or refuting protein predictions based on large-scale DNA and RNA sequencing efforts. This use of mass spectrometrically-derived sequence data for testing and refining predicted gene models has been termed proteogenomics. We report herein the application of proteogenomic methodology to a database of 10.9 million tandem mass spectra collec ...[more]

PMID: 22774004

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