Arabidopsis thaliana - Tiling Array Express
Visualizations of gene expression for Arabidopsis based on tiling array and cross-platform comparisons are available through tileViz.
To cite the developmental transcriptome data, please, refer to
Laubinger S., Zeller G., Henz S.R., Sachsenberg T., Widmer C.K., Naouar N., Vuylsteke M., Schölkopf B., Rätsch G. and Weigel D. (2008) At-TAX: a whole genome tiling array resource for developmental expression analysis and transcript identification in Arabidopsis thaliana, Genome Biology 9:R112. journal URL | pdf
For the abiotic stress data, please, cite
Zeller G., Henz S.R., Widmer C.K., Sachsenberg T., Rätsch G. and Weigel D. and Laubinger S. (2009) Stress-induced changes in the Arabidopsis thaliana transcriptome analyzed using whole genome tiling arrays, Plant Journal, 58(6):1068-1082. journal URL | pdf
For the small RNA mutant data, please, cite
Laubinger S., Zeller G., Henz S.R., Buechel S., Sachsenberg T., Wang J.-W., Rätsch G. and Weigel D. (2010) Global effects of the small RNA biogenesis machinery on the Arabidopsis thaliana transcriptome, Proc. Natl. Acad. Sciences USA, 107(41):17466-73. journal URL | pdf
Custom cdf files and example scripts for expression analysis with R / Bioconductor can be found here.
Raw and normalized array data, files containing the results of expression analysis as well as information on transcribed regions as predicted by mSTAD are available for download from our ftp server. Repeat data and definition files for the mapping of tiling probes to annotated gene models are also provided there (ftp server).
Abiotic stress data:
From our ftp server, raw and normalized array data (also in GEO format) are available. We also provide supplemental files with RMA expression values, lists of genes up- or downregulated under stress as well as lists for broad and narrow-response genes. Finally, you will find genome locations of transcriptionally active regions (TARs) there, as well as additional information on TARs, such as differential expression under stress.
Small RNA mutant data:
Tiling array data are available from our ftp server. Additionally files with RMA expression values, lists of genes up- or downregulated in mutants versus wild type are also provided. There is moreover data for expression of miRNA precursor transcripts for mutants and abiotic stress treatments. Finally, you will find genome locations of transcriptionally active regions (TARs) there, including TARs that accumulate in sRNA processing mutants relative to wild-type plants.
If you want to learn more about mSTAD, the segmentation method used for the detection of novel transcripts, please, have a look at the mSTAD homepage.