Affymetrix GeneChip Arabidopsis Genome [ATH1-121501]

Global Analysis of Arabidopsis Gene Expression Uncovers a Complex Array of Changes Impacting Pathogen Response and Cell Cycle during Geminivirus Infection

Computational design of host transcription-factors sets whose misregulation mimics the transcriptomic effect of viral infections.

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Effect of geminivirus Cabbage leaf curl virus on Arabidopsis Col-0 at 12 days post-inoculation during short day conditions.

infect

Transcription profiling by array of Arabidopsis infected with geminivirus Cabbage leaf curl virus

Hanley-Bowdoin ArabidopsisCaLCuV 12dpi

Effect of geminivirus Cabbage leaf curl virus on Arabidopsis Col-0 at 12 days post-inoculation during short day conditions.


Affymetrix:Protocol:ExpressionStat

Title: Affymetrix CHP Analysis (ExpressionStat). Description:

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-26718

Arabidopsis (Arabidopsis thaliana) Col-0 plants were grown on Metro-Mix 360 (SunGro) at 20°C in a Percival reach-in chamber (Series 101 without humidity controls) with a 8/16-h light/dark cycle under a light intensity of 17,000 Lux. For microarray experiments, plants with 16-18 true leaves were co-inoculated with Agrobacterium tumefaciens (strain A208::pTiC58-BI) transformed with pNSB1090 or pNSB1091, which contain T-DNAs with partial tandem copies of wild type CaLCuV A and B components, respectively (Egelkrout et al., 2002). The Agrobacterium transformants were inoculated from glycerol stocks (20 µl) and grown individually to saturation in Luria broth (LB) supplemented with 75 mg/mL spectinomycin at 28ºC overnight and then mixed 1:1. A drop of the mixed culture was deposited directly onto a wounded area generated by puncturing the rosette center 10 times with a 25 gauge needle. The meristematic region was avoided during the wounding process. Control plants were mock-inoculated using the same Agrobacterium strain transformed with pNSB690, which contains a 35S promoter uidA expression cassette. Typically, 12 plants were inoculated with CaLCuV while 6 were mock inoculated per tray. The tray was covered with a clear plastic lid for 4 days and then uncovered for the remainder of the growth period. Symptoms were monitored from the first day post-inoculation (dpi) until the CaLCuV-infected plants were dead at 6 weeks post infection. 

P-CAGE-26719

Leaves 7-9 at 12 days post-inoculation were harvested, pooled, flash frozen, ground in liquid nitrogen and stored at –80ºC. Three biological replicas corresponding to infected and mock-inoculated samples were collected and processed independently. Each replica contains 6 plants for mock-inoculated samples and 12 for virus-inoculated samples.

P-CAGE-26720

Total RNA was extracted from each sample using the Plant RNeasy Mini Kit (Qiagen).

P-CAGE-26721

Plants with 16-18 true leaves were co-inoculated with Agrobacterium tumefaciens (strain A208::pTiC58-BI) transformed with pNSB1090 or pNSB1091, which contain T-DNAs with partial tandem copies of wild type CaLCuV A and B components, respectively. The Agrobacterium transformants were inoculated from glycerol stocks (20 µl) and grown individually to saturation in Luria broth (LB) supplemented with 75 mg/mL spectinomycin at 28ºC overnight and then mixed 1:1. A drop of the mixed culture was deposited directly onto a wounded area generated by puncturing the rosette center 10 times with a 25 gauge needle. The meristematic region was avoided during the wounding process. Control plants were mock-inoculated using the same Agrobacterium strain transformed with pNSB690, which contains a 35S promoter uidA expression cassette. 

Global analysis of Arabidopsis gene expression uncovers a complex array of changes impacting pathogen response and cell cycle during geminivirus infection.

Transcription profiling by array of Arabidopsis infected with geminivirus Cabbage leaf curl virus

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