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CATMA, a comprehensive genome-scale resource for silencing and transcript profiling of Arabidopsis genes

Gert Sclep, Joke Allemeersch, Robin Liechti, Björn De Meyer UGent, Jim Beynon, Rishikesh Bhalerao, Yves Moreau, Wilfried Nietfeld, Jean-Pierre Renou, Philippe Reymond, et al. (2007) BMC BIOINFORMATICS. 8.
abstract
Background: The Complete Arabidopsis Transcript MicroArray (CATMA) initiative combines the efforts of laboratories in eight European countries [ 1] to deliver gene-specific sequence tags (GSTs) for the Arabidopsis research community. The CATMA initiative offers the power and flexibility to regularly update the GST collection according to evolving knowledge about the gene repertoire. These GST amplicons can easily be reamplified and shared, subsets can be picked at will to print dedicated arrays, and the GSTs can be cloned and used for other functional studies. This ongoing initiative has already produced approximately 24,000 GSTs that have been made publicly available for spotted microarray printing and RNA interference. Results: GSTs from the CATMA version 2 repertoire (CATMAv2, created in 2002) were mapped onto the gene models from two independent Arabidopsis nuclear genome annotation efforts, TIGR5 and PSB-EuGene, to consolidate a list of genes that were targeted by previously designed CATMA tags. A total of 9,027 gene models were not tagged by any amplified CATMAv2 GST, and 2,533 amplified GSTs were no longer predicted to tag an updated gene model. To validate the efficacy of GST mapping criteria and design rules, the predicted and experimentally observed hybridization characteristics associated to GST features were correlated in transcript profiling datasets obtained with the CATMAv2 microarray, confirming the reliability of this platform. To complete the CATMA repertoire, all 9,027 gene models for which no GST had yet been designed were processed with an adjusted version of the Specific Primer and Amplicon Design Software (SPADS). A total of 5,756 novel GSTs were designed and amplified by PCR from genomic DNA. Together with the pre-existing GST collection, this new addition constitutes the CATMAv3 repertoire. It comprises 30,343 unique amplified sequences that tag 24,202 and 23,009 protein-encoding nuclear gene models in the TAIR6 and EuGene genome annotations, respectively. To cover the remaining untagged genes, we identified 543 additional GSTs using less stringent design criteria and designed 990 sequence tags matching multiple members of gene families (Gene Family Tags or GFTs) to cover any remaining untagged genes. These latter 1,533 features constitute the CATMAv4 addition. Conclusion: To update the CATMA GST repertoire, we designed 7,289 additional sequence tags, bringing the total number of tagged TAIR6-annotated Arabidopsis nuclear protein-coding genes to 26,173. This resource is used both for the production of spotted microarrays and the large-scale cloning of hairpin RNA silencing vectors. All information about the resulting updated CATMA repertoire is available through the CATMA database http://www.catma.org.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
SEQUENCE TAGS, FUNCTIONAL GENOMICS, DNA-SEQUENCE, MICROARRAY, DATABASE, IDENTIFICATION, EXPRESSION, PROGRAM
journal title
BMC BIOINFORMATICS
BMC Bioinformatics
volume
8
article number
400
pages
13 pages
Web of Science type
Article
Web of Science id
000251902100001
JCR category
MATHEMATICAL & COMPUTATIONAL BIOLOGY
JCR impact factor
3.493 (2007)
JCR rank
3/24 (2007)
JCR quartile
1 (2007)
ISSN
1471-2105
DOI
10.1186/1471-2105-8-400
language
English
UGent publication?
yes
classification
A1
copyright statement
I have retained and own the full copyright for this publication
id
409512
handle
http://hdl.handle.net/1854/LU-409512
date created
2008-05-15 18:59:00
date last changed
2016-12-21 15:42:30
@article{409512,
  abstract     = {Background: The Complete Arabidopsis Transcript MicroArray (CATMA) initiative combines the efforts of laboratories in eight European countries [ 1] to deliver gene-specific sequence tags (GSTs) for the Arabidopsis research community. The CATMA initiative offers the power and flexibility to regularly update the GST collection according to evolving knowledge about the gene repertoire. These GST amplicons can easily be reamplified and shared, subsets can be picked at will to print dedicated arrays, and the GSTs can be cloned and used for other functional studies. This ongoing initiative has already produced approximately 24,000 GSTs that have been made publicly available for spotted microarray printing and RNA interference. 
Results: GSTs from the CATMA version 2 repertoire (CATMAv2, created in 2002) were mapped onto the gene models from two independent Arabidopsis nuclear genome annotation efforts, TIGR5 and PSB-EuGene, to consolidate a list of genes that were targeted by previously designed CATMA tags. A total of 9,027 gene models were not tagged by any amplified CATMAv2 GST, and 2,533 amplified GSTs were no longer predicted to tag an updated gene model. To validate the efficacy of GST mapping criteria and design rules, the predicted and experimentally observed hybridization characteristics associated to GST features were correlated in transcript profiling datasets obtained with the CATMAv2 microarray, confirming the reliability of this platform. To complete the CATMA repertoire, all 9,027 gene models for which no GST had yet been designed were processed with an adjusted version of the Specific Primer and Amplicon Design Software (SPADS). A total of 5,756 novel GSTs were designed and amplified by PCR from genomic DNA. Together with the pre-existing GST collection, this new addition constitutes the CATMAv3 repertoire. It comprises 30,343 unique amplified sequences that tag 24,202 and 23,009 protein-encoding nuclear gene models in the TAIR6 and EuGene genome annotations, respectively. To cover the remaining untagged genes, we identified 543 additional GSTs using less stringent design criteria and designed 990 sequence tags matching multiple members of gene families (Gene Family Tags or GFTs) to cover any remaining untagged genes. These latter 1,533 features constitute the CATMAv4 addition. 
Conclusion: To update the CATMA GST repertoire, we designed 7,289 additional sequence tags, bringing the total number of tagged TAIR6-annotated Arabidopsis nuclear protein-coding genes to 26,173. This resource is used both for the production of spotted microarrays and the large-scale cloning of hairpin RNA silencing vectors. All information about the resulting updated CATMA repertoire is available through the CATMA database http://www.catma.org.},
  articleno    = {400},
  author       = {Sclep, Gert and Allemeersch, Joke and Liechti, Robin and De Meyer, Bj{\"o}rn and Beynon, Jim and Bhalerao, Rishikesh and Moreau, Yves and Nietfeld, Wilfried and Renou, Jean-Pierre and Reymond, Philippe and Kuiper, Martin and Hilson, Pierre},
  issn         = {1471-2105},
  journal      = {BMC BIOINFORMATICS},
  keyword      = {SEQUENCE TAGS,FUNCTIONAL GENOMICS,DNA-SEQUENCE,MICROARRAY,DATABASE,IDENTIFICATION,EXPRESSION,PROGRAM},
  language     = {eng},
  pages        = {13},
  title        = {CATMA, a comprehensive genome-scale resource for silencing and transcript profiling of Arabidopsis genes},
  url          = {http://dx.doi.org/10.1186/1471-2105-8-400},
  volume       = {8},
  year         = {2007},
}

Chicago
Sclep, Gert, Joke Allemeersch, Robin Liechti, Björn De Meyer, Jim Beynon, Rishikesh Bhalerao, Yves Moreau, et al. 2007. “CATMA, a Comprehensive Genome-scale Resource for Silencing and Transcript Profiling of Arabidopsis Genes.” Bmc Bioinformatics 8.
APA
Sclep, G., Allemeersch, J., Liechti, R., De Meyer, B., Beynon, J., Bhalerao, R., Moreau, Y., et al. (2007). CATMA, a comprehensive genome-scale resource for silencing and transcript profiling of Arabidopsis genes. BMC BIOINFORMATICS, 8.
Vancouver
1.
Sclep G, Allemeersch J, Liechti R, De Meyer B, Beynon J, Bhalerao R, et al. CATMA, a comprehensive genome-scale resource for silencing and transcript profiling of Arabidopsis genes. BMC BIOINFORMATICS. 2007;8.
MLA
Sclep, Gert, Joke Allemeersch, Robin Liechti, et al. “CATMA, a Comprehensive Genome-scale Resource for Silencing and Transcript Profiling of Arabidopsis Genes.” BMC BIOINFORMATICS 8 (2007): n. pag. Print.