Affymetrix GeneChip Arabidopsis Genome [ATH1-121501]

Transcriptional profiling of mature Arabidopsis trichomes reveals that NOECK encodes the MIXTA-like transcriptional regulator MYB106

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Expression analysis of mature Arabidopsis trichomes in Col-0 and two mutants, triptychon (try-JC) and glabra3 (gl3-3)

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Transcription profiling of Arabidopsis trichomes from wild type, and tryptychon and glabra3 mutant plants

Expression analysis of mature Arabidopsis trichomes in Col-0 and two mutants, triptychon (try-JC) and glabra3 (gl3-3)


Affymetrix:Protocol:Hybridization-Unknown

P-AFFY-2

Labeling of samples was carried out according to the manufacturer’s standard protocol

P-AFFY-6

Title: Affymetrix CEL analysis. Description:

P-CAGE-26661

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.

P-CAGE-26662

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.

P-CAGE-26665

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].

P-CAGE-26666

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). 

Transcription profiling of Arabidopsis trichomes from wild type, and tryptychon and glabra3 mutant plants

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