Affymetrix GeneChip Arabidopsis Genome [ATH1-121501]

Heterogeneity of the Mitochondrial Proteome for Photosynthetic and Non-photosynthetic Arabidopsis Metabolism

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Microarray analysis of the changes in transcript abundance in cell culture and shoot

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Transcription profiling of Arabidopsis shoots, roots and cell cultures

Microarray analysis of the changes in transcript abundance in cell culture and shoot


Affymetrix:Protocol:ExpressionStat

Title: Affymetrix CHP Analysis (ExpressionStat). Description:

Affymetrix:Protocol:Hybridization-Unknown

P-AFFY-6

Title: Affymetrix CEL analysis. Description:

P-CAGE-26459

Arabidopsis cell suspension was cultured in growth medium (1x Murashige & Skoog medium without vitamins, 3% sucrose, 0.5mg/l naphthaleneacetic acid, 0.05mg/l kinetin, pH 5.8) in the dark for 7 days

P-CAGE-26460

Conditions for the hydroponic culture were adapted from Schlesier et al. (2003) with slight modifications. Approximately 50-100 wild type Arabidopsis thaliana seeds (ecotype Columbia) were surface-sterilized in 70% ethanol for 2 min followed by 15 min incubation in 5% bleach/0.1% Tween 20, inverting 5 times every 5 minutes. Seeds were then washed five times with sterilized water, and were carefully dispensed on a stainless steel wire mesh platform (mesh size 1 mm; 4 cm x 4 cmm x 2 cm) layered previously with 1% sterilized agarose in a round plastic vessel (diameter 68 mm, height 76 mm) containing approximately 60 ml liquid media (¼-strength Murashige & Skoog medium without vitamins, ¼-strength Gamborg B5 vitamins solution, 2mM MES, 0.5% [w/v] sucrose, pH 5.8). Arabidopsis plants were grown under 16/8 hr light/dark period with light intensity 100-125 umolm-2s-1 at 20oC over three weeks. Liquid medium was regularly replaced with freshly made liquid medium every seven days.

P-CAGE-26461

Detached roots harvested from hydroponic cultures were inoculated in growth medium (1xGamborgs B5 salt with vitamins, 3% [w/v] sucrose, pH 5.8) in the dark at 22oC for 5-6 weeks with constant shaking (95 rpm).

P-CAGE-26462

Total RNA was isolated using RNeasy plant mini protocol and RNase free DNase kit (QIAGEN, Clifton Hill, Victoria, Australia). The quality of isolated RNA was assessed by spectrophotometric analysis of A260/A280 ratio using ND-1000 UV-Vis Spectrophotometer (NanoDrop Technologies, Wilmingon, DE, USA) and qualitative analysis using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA).

P-CAGE-26463

The mRNA in 5 μg of total cellular RNA was converted to double-stranded cDNA using Superscript II with a T7-(dT) primer using One-Cycle cDNA Synthesis Kit (Affymetrix). The cDNA was in vitro transcribed to complementary RNA (cRNA) by incorporating biotin-UTP using the GeneChip IVT Labeling Kit (Affymetrix)

Transcription profiling of Arabidopsis shoots, roots and cell cultures

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