Affymetrix GeneChip Arabidopsis Genome [ATH1-121501]

Identification, and functional analysis of Ska2 interaction with the glucocorticoid receptor

Identification of novel genes in Arabidopsis involved in secondary cell wall formation using expression profiling and reverse genetics

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The aim of this experiment was to understand secondary cell wall formation as it is a major constituent of wood and plant fibres. To identify potential novel genes involved in this process, data has been generated from Arabidopsis stem, leaf and hypocotyl tissue undergoing varying amounts of secondary cell wall synthesis.

organism_part

Transcription profiling of Arabidopsis stem, leaf and hypocotyl tissue undergoing varying amounts of secondary cell wall synthesis

The aim of this experiment was to understand secondary cell wall formation as it is a major constituent of wood and plant fibres. To identify potential novel genes involved in this process, data has been generated from Arabidopsis stem, leaf and hypocotyl tissue undergoing varying amounts of secondary cell wall synthesis.


Affymetrix:Protocol:Hybridization-EukGE-WS2v4[]

Title: Affymetrix EukGE-WS2v4 Hybridization. Description:

P-AFFY-6

Title: Affymetrix CEL analysis. Description:

P-MEXP-2796

Expression analysis was performed using RMAExpress (02 release) using the background correction and quantile normalisation options (Bolstad, B.M., Irizarry R. A., Astrand, M., and Speed, T.P. (2003), A Comparison of Normalization Methods for High Density Oligonucleotide Array Data Based on Bias and Variance. Bioinformatics 19(2):185-193). In addition, scaling normalisation (target signal 100) using Affymetrix MAS 5.1 was done for the .CHP files submitted to this database.

P-MEXP-6065

P-MEXP-7305

Whole plants were removed from the soil and hypocotyls cut from the plant. Root material surrounding the hypocotyl was removed, the hypocotyl was washed with distilled water, dried and then immediately frozen in liquid nitrogen. The material was stored at -80oC until RNA extraction.

P-MEXP-7306

The third true leaf was harvested and immediately frozen in liquid nitrogen and then stored at -80oC until RNA extraction.

P-MEXP-7307

The siliques and flowers of the inflorescence stem were removed prior to the stem being divided into 4 sections of equal length. The base section was immediately frozen in liquid nitrogen and then stored at -80oC until RNAextraction.

P-MEXP-7308

The siliques and flowers of the inflorescence stem were removed prior to the stem being divided into 4 sections of equal length. The lower middle section was immediately frozen in liquid nitrogen and then stored at -80oC until RNAextraction.

P-MEXP-7309

The siliques and flowers of the inflorescence stem were removed prior to the stem being divided into 4 sections of equal length. The upper middle section was immediately frozen in liquid nitrogen and then stored at -80oC until RNAextraction.

P-MEXP-7310

The siliques and flowers of the inflorescence stem were removed prior to the stem being divided into 4 sections of equal length. The tip section was immediately frozen in liquid nitrogen and then stored at -80oC until RNAextraction.

P-MEXP-7311

Material from 9 plants was pooled. Total RNA extracted and purified with an RNeasy Plant Mini Kit (Qiagen, Hilden, Germany) according to manufacturer’s instructions. Resuspend in 50ul of array quality water. Synthesise cDNA with Superscript Double-Stranded cDNA Synthesis kit (Invitrogen, UK). Synthesise cRNA using the BioArray High Yield RNA transcript Labeling kit (Enzo Life Sciences Inc., NY) and apply to microarray. The experiment was performed in triplicate for each plant section using three independent pools of 9 plants i.e. biological replicates.

P-MEXP-7312

Material from 9 plants was pooled. Total RNA extracted and purified with an RNeasy Plant Mini Kit (Qiagen, Hilden, Germany) according to manufacturer’s instructions. Resuspend in 50ul of array quality water. Synthesise cDNA with Superscript Double-Stranded cDNA Synthesis kit (Invitrogen, UK). Synthesise cRNA using the BioArray High Yield RNA transcript Labeling kit (Enzo Life Sciences Inc., NY) and applied to microarray.

P-MEXP-7314

Arabidopsis (Lansberg-0 wt) plants were germinated and grown on plates containing 0.8-1.0% agar (w/v) and MS media with B5 vitamins for 11 daysprior to transferring 9 plants to a 4 inch pot containing compost with vermiculite and perlite (10:1:1). They were then grown in continuous light at 22oC in controlled environment cabinets (Percival, Ohio, USA) at a light intensity of 120-150 µE m-2. Material for the study of stem development was grown until the inflorescence stem contained 2 – 3 expanded siliques (18 days on soil). The siliques and flowers were removed prior to the stems being divided into 4 sections of equal length. Hypocotyls and leaves were harvested at the same developmental stage as stems. 

Transcription profiling of Arabidopsis stem, leaf and hypocotyl tissue undergoing varying amounts of secondary cell wall synthesis

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