Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

MRNA sequencing of Arabidopsis thaliana pdx3 mutants

ABSTRACT: Arabidopsis mutants in the PMP/PNP oxidase PDX3 show abberant growth and development. RNA sequencing reveals strong induction of stress-related genes in pdx3, particularly those associated with biotic stress. Whole rosettes (21- days old) of three biological replicates of wild-type and pdx3-3 (SALK_054167C) and pdx3-4 (GK-260E03) mutants, all ecotype Col-0, were sequenced and a differential gene expression analysis was performed.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Teresa Fitzpatrick

PROVIDER: E-GEOD-77428 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

mRNA sequencing of Arabidopsis thaliana pdx3 mutants

Project description:Arabidopsis mutants in the PMP/PNP oxidase PDX3 show abberant growth and development.RNA sequencing reveals strong induction of stress-related genes in pdx3, particularly those associated with biotic stress.

2016-02-02 | GSE77428 | GEO

Citrullination of glucokinase is linked to autoimmune diabetes

Project description:Inflammation, including reactive oxygen species and inflammatory cytokines in tissues amplify various post-translational modifications (PTMs) of self-proteins. A number of PTMs have been identified as autoimmune biomarkers in the initiation and progression of Type 1 diabetes (T1D). In this study, we have identified the citrullination of pancreatic glucokinase (GK) as a result of inflammation, triggering autoimmunity and affecting GK biological functions. Glucokinase is expressed in hepatocytes to regulate glycogen synthesis, and in pancreatic beta cells as a glucose sensor to initiate glycolysis and insulin signaling. We identify autoantibodies and autoreactive CD4+ T cells to glucokinase epitopes in the circulation of T1D patients and NOD mice. Finally, citrullination alters GK biologic activity (Km) and suppresses glucose-stimulated insulin secretion. Our studies define glucokinase as a T1D biomarker, providing new insights of how inflammation drives PTMs to create both neoautoantigens and affect beta cell metabolism.

2022-03-17 | PXD028825 | Pride

Transcriptomic Analysis of pnp-1 mutants in C. elegans

Project description:We used RNA-seq to identify gene expression changes in C. elegans pnp-1 mutants

2021-04-14 | GSE165786 | GEO

Transcriptome-wide analysis of gene expression in dark-grown WT and pif mutant seedlings

Project description:We sequenced mRNA from WT and PhytochromeInteractingFactor (pif) mutant seedlings grown for 2d in darkness. Transcriptome profiles of the wild-type (WT), pif1, pif3, pif, pif5 monogenic mutants, pif3pif4pif5 (pif345), pif1pif4pif5(pif145), pif1pif3pif5 (pif135) and pif1pif3pif4 (pif134) triple mutants and pif1pif3pif4pif5 (pifq) quadruple mutant seedlings. Biological triplicate samples were analyzed from libraries constructed using a 3'-capture, 5' to 3' directional method.

2014-10-02 | E-GEOD-42665 | biostudies-arrayexpress

Transcription profiling by array of Staphylococcus aureus wild type and rnc, pnp and sigB mutants

Project description:Transcriptome mapping of Staphylococcus aureus wild type and rnc, pnp and sigB mutants

2010-12-31 | E-MEXP-2778 | biostudies-arrayexpress

Small RNA accumulation in Transposable Element-silent and Transposable Element-active epigenomes

Project description:Background: The small RNAs that Transposable Elements generate are vastly different when they are transcriptionally silenced compared to when they are transcriptionally activated. We performed the deep sequencing of small RNAs in a number of small RNA biogenesis mutants in both Transposable Element-silenced and Transposable Element-active epigenome backgrounds. Results: We found that Transposable Elements generate large amounts of 21-22nt siRNAs only when they are transcriptionally active. These 21-22nt siRNAs are incorporated into the AGO6 protein. Conclusion: Ago6 is the key protein that bridges the post-transcriptional degradation of Transposable Element mRNAs and the establishment of DNA methylation. Examination of flower bud small RNAs from wild type and 5 single or double mutant combinations, many of which have biological replicates. In addition, IP purification of the AGO6 protein (and mock no-antigen controls) followed by sequencing of the incorporated small RNAs. Replicate A for Col and ddm1 are submitted in GSE41755

2014-11-14 | E-GEOD-57191 | biostudies-arrayexpress

Genome-wide analysis of LINK1 and LINK2 effects on the Arabidopsis transcriptome

Project description:The goal of this study was to compare the transcriptional profile (RNA-seq) of wild type plants with that of link1link2 double mutants grown under continous light or long day (16h light/8 h darkness) conditions. In the first experiment wild-type and link1link2 mutant plants were grown for two weeks under continuous white light conditions at 22 degrees centigrades and the transcriptional profile of these plants was analyzed using RNA-seq. In the second experiment, wild-type and link1link2 mutants were grown under long day conditions (16 h light/8 h darkness), and the transcriptional profile of these plants was analyzed in samples harvested every 4 hours over a 24 hour time-course, starting 2 hours after the onset of the light period.

2013-08-02 | E-GEOD-43865 | biostudies-arrayexpress

Comparative transcriptome profiling of Arabidopsis lyrata and Arabidopsis thaliana

Project description:Arabidopsis thaliana and Arabidopsis lyrata are two closely related Brassicaceae species, which are used as models for plant comparative biology. They differ by lifestyle, predominant mating strategy, ecological niches and genome organization. In order to explore molecular basis of specific traits, we performed RNA-sequencing of vegetative rosettes from both species. Additionally, we sequenced apical meristems and inflorescences of A. lyrata that allow for intra-specific transcriptome comparison in several major developmental stages. Arabidopsis lyrata and Arabidopsis thaliana aerial tissues were collected from mock treated plants, total RNA isolated and poly-A RNA populations sequenced

2015-08-01 | E-GEOD-69222 | biostudies-arrayexpress

m6A level and isoform characterization sequencing (m6A-LAIC-seq) reveal the census and complexity of the m6A epitranscriptome

Project description:N6-methyladenosine (m6A) is a widespread reversible chemical modification of RNAs, implicated in many aspects of RNA metabolism. Little quantitative information exists as to either how many transcript copies of particular genes are m6A modified (âm6A levelsâ), or the relationship of m6A modification(s) to alternative RNA isoforms. To deconvolute the m6A epitranscriptome, we developed m6A level and isoform-characterization sequencing (m6A-LAIC-seq). We found that cells exhibit a broad range of non-stoichiometric m6A levels with cell type specificity. At the level of isoform characterization, we discovered widespread differences in use of tandem alternative polyadenylation (APA) sites by methylated and nonmethylated transcript isoforms of individual genes. Strikingly, there is a strong bias for methylated transcripts to be coupled with proximal APA sites, resulting in shortened 3â untranslated regions (3â-UTRs), while nonmethylated transcript isoforms tend to use distal APA sites. m6A-LAIC-seq yields a new perspective on transcriptome complexity and links APA usage to m6A modifications. m6A-LAIC-seq of H1-ESC and GM12878 cell lines, each cell line has two replicates

2016-06-24 | E-GEOD-66086 | biostudies-arrayexpress

Non-CG methylation patterns shape the epigenetic landscape in Arabidopsis

Project description:DNA methylation occurs in both CG and non-CG sequence contexts. Non-CG methylation is abundant in plants, and is mediated by CHROMOMETHYLASE (CMT) and DOMAINS REARRANGED METHYLTRANSFERASE (DRM) proteins; however its roles remain poorly understood. Here we characterize the roles of non-CG methylation in Arabidopsis thaliana. We show that a poorly characterized methyltransferase, CMT2, is a functional methyltransferase in vitro and in vivo. CMT2 specifically binds histone H3 lysine 9 (H3K9) dimethylation and methylates non-CG cytosines at sites that are also regulated by H3K9 dimethylation. By generating different combinations of non-CG methylation mutants, we reveal the contributions and redundancies between each methyltransferase in DNA methylation patterning and in regulating transposable elements (TEs) and protein-coding genes. We also demonstrate extensive dependencies of small RNA accumulation and H3K9 methylation patterning on non-CG methylation, suggesting self-reinforcing mechanisms between these epigenetic factors. The results suggest that non-CG methylation patterns are critical in shaping the histone modification and small non-coding RNA landscapes. Eighteen mRNA-seq samples, five smRNA-seq samples, five bisulfite-seq samples, twenty ChIP-seq samples. Bisulfite-seq data for cmt2-7 single mutants, cmt3 single mutants, drm1/2 double mutants, drm1/2 cmt3 triple mutants are deposited in GSE39901. Processed wiggle format files for all datasets can be downloaded at http://genomes.mcdb.ucla.edu/AthBSseq/

2013-12-15 | E-GEOD-51304 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data