{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Marc Jakoby"],"organism":["Arabidopsis thaliana"],"software":["MicroArraySuite 5.0"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-ATMX-33"],"description":["Expression analysis of mature Arabidopsis trichomes in Col-0 and two mutants, triptychon (try-JC) and glabra3 (gl3-3)"],"repository":["biostudies-arrayexpress"],"sample_protocol":["Hybridization - Title: Affymetrix Generic Hybridization. Description:","Nucleic Acid Extraction - Primary leaves were attached to slides with double sided tape and frozen on dry ice. Trichomes were clipped off at their stem leaving their base on the leaf in order to avoid contamination with adjacent epidermal or mesophyll cells using extra fine forceps and immediately transferred to RLT buffer (Qiagen, Hilden, Germany). RNA was isolated using the RNeasy Micro kit (Qiagen). RNA was quantified with an Agilent Bioanalyzer and the Nano6000 chips. 50 to 100 ng of total RNA were used as starting material for the RNA amplifications following the Affymetrix protocol for the amplification of eucaryote RNA.","Labeling - Title: Affymetrix in vitro transcription. Description:","Nucleic Acid Extraction - Primary leaves were attached to slides with double sided tape and frozen on dry ice and the trichomes were removed with a small brush. Leaves were removed from the slides, washed shortly in water and transferred to RLT buffer. RNA was isolated using the RNeasy Micro kit (Qiagen).","Growth Protocol - Seeds were sown on soil and pots were stored at 4 °C for 3 days. Plants for profiling experiments were grown in a climate chamber for 13 days at a 10 h light / 14 h dark cycle at 23 °C."],"figure_sub":["MIAME Score","Raw Data","Organization","Assays and Data","MAGE-TAB Files","Array Designs"],"data_protocol":["Feature Extraction - Title: Affymetrix CEL analysis. Description:","Assay Data Transformation - All statistical analyses of the microarray data were conducted in R (www.r-project.org) employing BioConductor (www.bioconductor.org) facilities. Probesets of the triplicates were summarized with the MAS-5.0 algorithm. Probesets with a differences between the Col-0 trichome samples higher than two-fold were excluded from the analysis. The MAS 5.-0 summaries of the remaining 18,459 probesets of the Col-0 trichome GeneChips and of the gl3-3 and try-JC mutant triplicates were normalized against the mean of the leaves whose trichomes were removed (LwoT) control group employing a LOESS smoother operating on logarithmic M-A scale [Cleveland, 1979]."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"pubmed_abstract":["Leaf hairs (trichomes) of Arabidopsis (Arabidopsis thaliana) have been extensively used as a model to address general questions in cell and developmental biology. Here, we lay the foundation for a systems-level understanding of the biology of this model cell type by performing genome-wide gene expression analyses. We have identified 3,231 genes that are up-regulated in mature trichomes relative to leaves without trichomes, and we compared wild-type trichomes with two mutants, glabra3 and triptychon, that affect trichome morphology and physiology in contrasting ways. We found that cell wall-related transcripts were particularly overrepresented in trichomes, consistent with their highly elaborated structure. In addition, trichome expression maps revealed high activities of anthocyanin, flavo"],"study_type":["transcription profiling by array"],"species":["Arabidopsis thaliana"],"pubmed_title":["Transcriptional profiling of mature Arabidopsis trichomes reveals that NOECK encodes the MIXTA-like transcriptional regulator MYB106"],"pubmed_authors":["Jakoby MJ, Falkenhan D, Mader MT, Brininstool G, Wischnitzki E, Platz N, Hudson A, Hülskamp M, Larkin J, Schnittger A.","Marc Jakoby"],"additional_accession":[]},"is_claimable":false,"name":"Transcription profiling of Arabidopsis trichomes from wild type, and tryptychon and glabra3 mutant plants","description":"Expression analysis of mature Arabidopsis trichomes in Col-0 and two mutants, triptychon (try-JC) and glabra3 (gl3-3)","dates":{"release":"2008-09-23T00:00:00Z","modification":"2022-02-02T18:26:44.032Z","creation":"2022-02-02T18:26:44.032Z"},"accession":"E-ATMX-33","cross_references":{"pubmed":["18805951"],"EFO":["EFO_0002768"],"doi":["10.1104/pp.108.126979"]}}