Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

46 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ACCESS DATA

Json Xml

Publications

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

Similar Datasets

Transcriptome analysis during the shift from dark to blue light in Arabidopsis wild type Col-0 plants.

Project description:RNA-seq was performed in three-day-old wild-type Col-0 plants grown on filter paper in the dark that were exposed to blue light and harvested after one-hour exposure.

2015-10-09 | E-MTAB-5188 | biostudies-arrayexpress

Zea mays Transcriptome or Gene expression

Project description:To discover the transcriptional dynamics during seed germination we have obtained the time course transcriptomes for embryonic shoot apical meristem (SAM) every six hours, starting from dry seeds to hour 72 (3 days).

2013-04-02 | E-MTAB-4205 | biostudies-arrayexpress

RNA from lung and BAL cells of wildtype mice infected with influenza

Project description:Characterisation of lung and bronchial alveolar lavage (BAL) fluid of wildtype mice infected with influenzaThese data are part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

2015-10-06 | E-ERAD-397 | biostudies-arrayexpress

Medicago truncatula Transcriptome or Gene expression

Project description:Our global transcriptomic approach to study Myc-LCO signalling in M. truncatula used an experimental design of three genotypes â A17 (WT), dmi3 and nsp1 â and three treatments â sulphated Myc-LCOs (S Myc-LCOs), nonsulphated Myc-LCOs (NS Myc-LCOs), and solvent controls (acetonitrile, ACN). We pooled two early treatment time points (2 + 4 h) based on preliminary data and reports of transcriptional changes occurring within hours of Myc-LCO treatment. Three biological replicates were sequenced per condition. We used M. truncatula dmi3 and nsp1 mutants, described originally as NodâMycâ and NodâMyc+, respectively, and the two major types of Myc-LCOs (sulphated and nonsulphated) to determine overlaps and specificities of Myc-LCO responses. Myc-LCOs were used at 10â6 M because they are biologically active at about a 100-fold higher concentration than Nod factors, which have been used at 10â7, 10â8 M in transcriptomic studies.

2014-06-24 | E-MTAB-5182 | biostudies-arrayexpress

SAD1 dynamically regulates alternative splicing and stress tolerance

Project description:Although Sm-like proteins (LSMs) form the core of U6 RNPs and function in pre-mRNA splicing, little is known regarding their regulatory role in selection of splice sites, alternative splicing (AS) and splicing efficiency in eukaryotes. The Arabidopsis SAD1 locus encodes the LSM5 protein and was defined in a genetic screen for components that regulate the expression of stress-responsive gene. To further investigate regulatory role of the protein SAD1 in pre-mRNA splicing, we performed RNA sequencing (RNA-seq) to examine the changes of the global alternative splicing (AS) among the wildtype Arabidopsis plant (C24), the mutant plant (sad1) and the sad1-overexpressed plant (SAD1-OE). Our work not only provided novel insights into the regulatory role of SAD1 or LSM proteins in splicing, but also provided new cues to improving splicing efficiency and optimizing biological functions and screening the stress-resistant plant.

2013-11-01 | E-MTAB-4336 | biostudies-arrayexpress

Transcriptome profiling of embryos from the Mouse Genetics Project DMDD

Project description:Total RNA was extracted from wildtype embryos of developmental stage E14.5 for baseline expression study relating to the Mouse Genetics Project (http://www.dmdd.org.uk/). Protocol: After DNase treatment, fragmented RNA was enriched for the 3 ends by pull down using an anchored polyT oligo attached to magnetic beads. An RNA oligo comprising part of the Illumina adapter 1 was ligated to the 5 end of the captured RNA and the RNA was eluted from the beads. Reverse transcription was primed with an anchored polyT oligo with part of Illumina adapter 2 at the 5 end followed by 10 bases HBDVHBDVHB (using the single base code), then one of 96 eight base indexing tags, then CG and 14 T bases. An Illumina library with full adapter sequence was produced by 20 cycles of PCR. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

2014-07-28 | E-ERAD-278 | biostudies-arrayexpress

Transcriptome profiling of zebrafish neural crest mutants

Project description:Total RNA was extracted from morpholigcally abnormal and wildtype sibling larvae of neural crest mutants derived from ENU mutagenesis. The 3 end of fragmented RNA was pulled down using polyT oligos attached to magnetic beads, reverse transcribed, made into Illumina libraries and sequenced using Illumina HiSeq paired-end sequencing. Protocol: Total RNA was extracted from zebrafish embryos using Trizol and DNase treated. Chemically fragmented RNA was enriched for the 3 ends by pulled down using an anchored polyT oligo attached to magnetic beads. An RNA oligo comprising part of the Illumina adapter 2 was ligated to the 5 end of the captured RNA and the RNA was eluted from the beads. Reverse transcription was primed with an anchored polyT oligo with part of Illumina adapter 1 at the 5 end followed by 12 random bases, then an 8 base indexing tag, then CG and 14 T bases. An Illumina library with full adapter sequence was produced by 20 cycles of PCR. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

2014-04-28 | E-ERAD-243 | biostudies-arrayexpress

Transcriptome profiling of zebrafish muscle mutants

Project description:Total RNA was extracted from mutant and wildtype sibling larvae of one or more alleles of zebrafish muscle mutants. The 3' ends of fragmented RNA were pulled down using polyT oligos attached to magnetic beads, reverse transcribed, made into Illumina libraries and sequenced using IlluminaHiSeq paired-end sequencing. Protocol: Total RNA was extracted and DNase treated. Fragmented RNA was enriched for the 3 ends by pull down using a polyT oligo attached to magnetic beads. An RNA oligo comprising part of the Illumina adapter 2 was ligated to the 5 end of the captured RNA and the RNA was eluted from the beads. Reverse transcription was primed with an anchored polyT oligo with part of Illumina adapter 1 at the 5 end followed by 12 random bases, then an 8 base indexing tag, then CG and 14 T bases. An Illumina library with full adapter sequence was produced by PCR. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

2015-07-14 | E-ERAD-374 | biostudies-arrayexpress

Transcriptome and Metabolite Profiling of the Infection Cycle of Zymoseptoria tritici on Wheat Reveals a Biphasic Interaction with Plant Immunity Involving Differential Pathogen Chromosomal Contributions and a Variation on the Hemibiotrophic Lifestyle Definition.

Project description:The hemibiotrophic fungus Zymoseptoria tritici causes Septoria tritici blotch disease of wheat (Triticum aestivum). Pathogen reproduction on wheat occurs without cell penetration, suggesting that dynamic and intimate intercellular communication occurs between fungus and plant throughout the disease cycle. We used deep RNA sequencing and metabolomics to investigate the physiology of plant and pathogen throughout an asexual reproductive cycle of Z. tritici on wheat leaves. Over 3,000 pathogen genes, more than 7,000 wheat genes, and more than 300 metabolites were differentially regulated. Intriguingly, individual fungal chromosomes contributed unequally to the overall gene expression changes. Early transcriptional down-regulation of putative host defense genes was detected in inoculated leaves. There was little evidence for fungal nutrient acquisition from the plant throughout symptomless colonization by Z. tritici, which may instead be utilizing lipid and fatty acid stores for growth. However, the fungus then subsequently manipulated specific plant carbohydrates, including fructan metabolites, during the switch to necrotrophic growth and reproduction. This switch coincided with increased expression of jasmonic acid biosynthesis genes and large-scale activation of other plant defense responses. Fungal genes encoding putative secondary metabolite clusters and secreted effector proteins were identified with distinct infection phase-specific expression patterns, although functional analysis suggested that many have overlapping/redundant functions in virulence. The pathogenic lifestyle of Z. tritici on wheat revealed through this study, involving initial defense suppression by a slow-growing extracellular and nutritionally limited pathogen followed by defense (hyper) activation during reproduction, reveals a subtle modification of the conceptual definition of hemibiotrophic plant infection.

2015-03-12 | E-MTAB-4116 | biostudies-arrayexpress

Oryza sativa strain:Nipponbare Transcriptome or Gene expression

Project description: Not available

2014-11-04 | E-MTAB-4123 | biostudies-arrayexpress