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

Transcription profiling of Arabidopsis thaliana seedlings using different Affymetrix RNA labelling protocols

ABSTRACT: Here we compare transcriptomic data generated using Affymetrix one-cycle (standard labelling protocol), two-cycle (small-sample protocol) and IVT-Express protocols with the Affymetrix ATH1 array using Arabidopsis root samples. Results obtained with each protocol are broadly similar. However, we show that there are 35 probe sets (of a total of 22810) that are misrepresented in the two-cycle data sets. Of these, 33 probe sets were classed as mis-amplified when comparisons of two independent publicly available data sets were undertaken.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Michael Wilson

PROVIDER: E-MEXP-2608 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Shared Molecules

Only show the datasets with similarity scores above: 0.5

Threshold

0.5

Similar Datasets

Transcription profiling by array of Arabidopsis wild type and an ARF7/ARF19 double knockout mutant roots dissected into 5 developmental zones

Project description:Arabidopsis seedlings, of both wild-type and an ARF7/ARF19 double knockout mutant, were grown to 7 days post-germination. The roots were then dissected into 5 developmental zones, the meristem, early elongation zone, late elongation zone, mature root and lateral root zone. The sections then underwent transcriptional profiling to identify processes and regulatory events specific and in common to the zones.

2011-04-13 | E-MEXP-2912 | biostudies-arrayexpress

A timecourse of IAA treatment on the Arabidopsis root tip

Project description:A timecourse of IAA treatment on the Arabidopsis root tip

2013-05-12 | E-MTAB-1354 | biostudies-arrayexpress

CPIB Lateral Root timecourse

Project description:In Arabidopsis, lateral roots (LRs) originate from pericycle cells located adjacent to vascular tissues, deep within the primary root. Consequently, new LR organs have to emerge through several overlying tissues. Eight stages of LR primordium development have been defined, with stage I representing a single layer of primordium cells generated by the first round of asymmetric divisions and stage VIII defining primordia that have fully emerged through the outer cell layers. To identify novel genes involved in LR development, we generated a transcriptomic time course dataset encompassing each LR developmental stage from pre-initiation to post-emergence.

2015-02-01 | E-MTAB-2565 | biostudies-arrayexpress

Analysis of polyploidy-associated transcriptional gene silencing (paTGS) mutants

Project description:A case of transcriptional gene silencing, originally observed in tetraploid Arabidopsis plants, created an epiallele resistant to many mutations or inhibitor treatments that activate other suppressed genes. This raised the question about the molecular basis of this extreme stability. A combination of forward and reverse genetics, transcriptome profiling and drug application provides evidence for a double safeguard system that is only alleviated upon the simultaneous removal of both DNA methylation and histone methylation by loss of DDM1 or HOG1 acitivity. Three biological replicates per line are provided. C2S1 = Wt line; hog1-7=774; ddm1-12=1135

2010-02-01 | E-GEOD-17496 | biostudies-arrayexpress

Transcription profiling of Arabidopsis roots from wild type and stop1 mutant plants treated with Al or low pH

Project description:Comparison of stop1 mutant vs. wild type treated with Al or low pH, and gene expression responses to rhizotoxic ions (Al, low pH) in Arabidopsis roots.

2009-05-04 | E-MEXP-1908 | biostudies-arrayexpress

Transcription profiling of Arabidopsis roots after treatment with rhizotoxic ions Al, Cu, Cd and NaCl

Project description:Comparison of gene expression responses to rhizotoxic ions (Al, Cu, Cd and NaCl) in Arabidopsis roots.

2009-05-04 | E-MEXP-1907 | biostudies-arrayexpress

WRKY43 regulates polyunsaturated fatty acid content and abiotic stress tolerance of Arabidopsis seeds

Project description:Loss of the seed-specific WRKY transcription factor WRKY43 confers enhanced tolerance towards high salt, high osmolarity and low temperature with respect to seed germination. wrky43 loss of function lines display increased inhibition of seed germination in response to exogenous ABA, while WRKY43 overexpression lines are more tolerant towards exogenous ABA. The opposing effect of the wrky43 mutant on salt and ABA tolerance is reminiscent of fatty acid desaturase mutants. Loss of WRKY43 enhances polyunsaturated fatty acid content, particularly 18:2 and 18:3 in TAGs and Phospholipids. Gene chip arrays show that ABA-induced regulation of FUSCA3, ZAT10 and seed storage proteins are absent in the wrky43 mutant. Promoter-Luciferase studies confirm direct regulation of ZAT10 by WRKY43 and suggest indirect regulation of FUS3 and SSPs. In summary WRKY43 acts as a positive regulator of ABA-dependent gene regulation and of fatty acid desaturation that finally results in enhanced tolerance to abiotic stress. 2 biological replicates of Arabidopsis thaliana Ler-0 wildtype and wrky43 muatnt seeds were compared after incubation in liquid 0.5 MS media with 2 ÂµM ABA for 4 days

2016-08-16 | E-GEOD-72154 | biostudies-arrayexpress

Transcription profiling by array of Medicago truncatula border cells, root tips and whole roots

Project description:To better understand the spatial distribution of gene expression network in legume roots, transcriptomics profiles of border cells, root tips and whole roots were compared.

2011-08-20 | E-MEXP-2883 | biostudies-arrayexpress

Transcription profiling of Scarecrow mutant Arabidopsis root-tips of 5-day-old plants to those of wildtype reveals an evolutionarily conserved mechanism delimiting SHR movement defines a single layer of endodermis in plants

Project description:Comparison of Scarecrow mutant Arabidopsis root-tips of 5-day-old plants to those of wildtype.

2009-06-04 | E-MEXP-2208 | biostudies-arrayexpress

The tinkerbell (tink) mutation identifies the dual-specificity MAPK phosphatase INDOLE-3-BUTYRIC ACID-RESPONSE5 (IBR5) as a novel regulator of organ size in Arabidopsis.

Project description:Mitogen-activated dual-specificity MAPK phosphatases are important negative regulators in the MAPK signalling pathways responsible for many essential processes in plants. In a screen for mutants with reduced organ size we have identified a mutation in the active site of the dual-specificity MAPK phosphatase INDOLE-3-BUTYRIC ACID-RESPONSE5 (IBR5) that we named tinkerbell (tink) due to its small size. Analysis of the tink mutant indicates that IBR5 acts as a novel regulator of organ size that changes the rate of growth in petals and leaves. Organ size and shape regulation by IBR5 acts independently of the KLU growth-regulatory pathway. Microarray analysis of tink/ibr5-6 mutants identified a likely role for this phosphatase in male gametophyte development. We show that IBR5 may influence the size and shape of petals through auxin and TCP growth regulatory pathways. 6 samples, three mutant replicates, three wild type replicates.

2015-07-30 | E-GEOD-66419 | 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