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CATMA specifications

Information


Unique identifier OMICS_03266
Name CATMA
Alternative name Complete Arabidopsis Transcriptome MicroArray
Restrictions to use None
Maintained Yes

Taxon


  • Plants and Fungi
    • Arabidopsis thaliana

Maintainer


  • person_outline Martin Kuiper

Publication for Complete Arabidopsis Transcriptome MicroArray

CATMA citations

 (12)
library_books

Arabidopsis HEAT SHOCK TRANSCRIPTION FACTORA1b overexpression enhances water productivity, resistance to drought, and infection

2013
J Exp Bot
PMCID: 3733161
PMID: 23828547
DOI: 10.1093/jxb/ert185

[…] RNA extraction from rosettes of four pooled plants, and the comparison of Col-0 versus HSFA2Ox was carried out using the CATMA (version 3) microarray (). Normalization and analysis of the array was carried out using LimmaGUI, a graphical front end for the limma (Linear Models for MicroArray; ) package for R available fr […]

call_split

Identification of novel transcription factors regulating secondary cell wall formation in Arabidopsis

2013
Front Plant Sci
PMCID: 3677987
PMID: 23781226
DOI: 10.3389/fpls.2013.00189
call_split See protocol

[…] Four in house microarray datasets were generated in our laboratory. In brief, datasets are from wat1 T-DNA Arabidopsis mutant CATMA microarray (Ranocha et al., ); EgMYB1 (Legay et al., ), EgMYB2 over-expressed in Arabidopsis (unpublished), and orthologs of Eucalyptus xylem expressed genes (Rengel et al., ). Publicly availabl […]

call_split

A local regulatory network around three NAC transcription factors in stress responses and senescence in Arabidopsis leaves

2013
Plant J
PMCID: 3781708
PMID: 23578292
DOI: 10.1111/tpj.12194
call_split See protocol

[…] Total RNA was extracted from four leaves per line, labelled and hybridized to CATMA v4 arrays (Allemeersch et al., ; http://www.catma.org) as described (Breeze et al., ). For analysis of Col-0, myb2 and myb108 samples four replicates were pooled and labelled twice with each dye […]

library_books

Genetical Genomics Reveals Large Scale Genotype By Environment Interactions in Arabidopsis thaliana

2013
Front Genet
PMCID: 3541481
PMID: 23335938
DOI: 10.3389/fgene.2012.00317

[…] aminoallyl)-dUTP and labeled with either Cy3 or Cy5 mono-reactive dye (Amersham, Piscataway, USA). All cDNA products were purified using the QIAquick PCR purification Kit (Qiagen, Valencia, USA). The CATMA (Allemeersch et al., ) Arabidopsis DNA microarrays were provided by Utrecht University (the Netherlands) and were produced from a set of 150-450-mers representing 20833 unique genes. Arrays were […]

library_books

Signal Molecules Mediate the Impact of the Earthworm Aporrectodea caliginosa on Growth, Development and Defence of the Plant Arabidopsis thaliana

2012
PLoS One
PMCID: 3513312
PMID: 23226498
DOI: 10.1371/journal.pone.0049504

[…] verse transcribed in the presence of 200 U Superscript II (Invitrogen, Carlslab, U.S.A.), cy3-dCTP and cy5-dCTP (NEN, Boston, U.S.A.) and hybridized on Complete Arabidopsis Transcriptome MicroArrays (CATMA), each with 24576 Gene Specific Tags from A. thaliana , with a dye swap to avoid dye bias . After an array-by-array normalization, a global intensity-dependent normalization and a correction of […]

library_books

A Meta Analysis Reveals the Commonalities and Differences in Arabidopsis thaliana Response to Different Viral Pathogens

2012
PLoS One
PMCID: 3395709
PMID: 22808182
DOI: 10.1371/journal.pone.0040526

[…] re measured 8 dpi from Col-0 leaves. TCV data (two-color raw data, three replicates, NCBI GEO accession GSE29387) were quantified 10 dpi in Col-0 plants. These two data sets were normalized using the CATMA BGS procedure , and the list of differentially expressed genes was obtained by performing a Limma test with FDR correction (adjusted P<0.05). In addition, for TCV data, a fold-change criterion o […]

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CATMA institution(s)
Department of Plant Systems Biology, VIB, Ghent, Belgium

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