Affymetrix GeneChip Soybean Genome Array

The Soybean Rhg1 Locus for Resistance to the Soybean Cyst Nematode Heterodera glycines Regulates the Expression of a Large Number of Stress- and Defense-Related Genes in Degenerating Feeding Cells

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processedData

Comparison of syncytia gene expression between soybean near-isogenic lines 7923R (NIL-R) and 7923S (NIL-S) infected with the soybean cyst nematode (PA3).

genotype

time since innoculation

Transcription profiling by array of soybean NIL-R vs NIL-S captured syncitia after infection with soybean cyst nematode

Mitchum Soybean NIL-R vs NIL-S Captured Syncytia

Comparison of syncytia gene expression between soybean near-isogenic lines 7923R (NIL-R) and 7923S (NIL-S) infected with the soybean cyst nematode (PA3).


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-MTAB-41863

P-MTAB-41864

Two-day-old seedlings with a 2-3cm long uniform root were inoculated with freshly hatched nematodes according to Mahalingam et al. (1998), with the following modifications. Cysts of SCN were extracted from infested soil by flotation in water and collected on a 250ƒÝm (No.60) sieve. Harvested cysts were gently crushed using a drill press and the eggs collected on a 25ƒÝm (No. 500) sieve (Faghihi and Ferris, 2000) and further purified on a sucrose density gradient. The eggs were sterilized in 0.02% sodium azide for 20 min and washed extensively in sterile water to remove any traces of sodium azide. Pre-parasitic second stage juveniles (J2) were isolated by hatching eggs in the presence of 1.5mg/ml gentamycin and 0.05mg/ml nystatin at 28oC on a modified Baermann pan for two days. Hatched juveniles were collected, rinsed with sterile water, and suspended in 0.1% sterile agarose. One hundred microliters of 0.1% agarose containing 300 ¡Ó 25 pre-parasitic J2 was applied approximately 1cm above the root tip of each soybean root which was marked with a dot using a black sharpie pen. Infection was synchronized by washing the infected roots with water exactly 24 hours after inoculation. Samples were collected at 5 and 8 days-post-inoculation (dpi). 

P-MTAB-41865

Because a syncytium is made up of a complex of fused cells, and the number of cells incorporated into the syncytium increases over time, it is difficult to determine the exact number of individual cells (or individual syncytia) required to obtain a sufficient amount of amplified cRNA for microarray hybridization. Therefore, we evaluated the correlation between the amount of captured syncytial cells and the quantity of amplified RNA recovered by comparing the cRNA yield obtained from 16 independent LCM experiments to the surface area of the LCM cap covered by captured syncytial cells. To estimate the area covered by the syncytial cells on each cap, all caps were photographed at the same magnification and cap images were analyzed and the area calculated using image analysis software. Regression analysis yielded a correlation coefficient of 0.90 indicating a strong positive linear relationship between the RNA yield and corresponding syncytial cell area harvested by LCM. These results indicated that approximately 7 micrograms of amplified cRNA could be obtained per square millimeter captured cell area. 

P-MTAB-41866

The Soybean Rhg1 locus for resistance to the soybean cyst nematode Heterodera glycines regulates the expression of a large number of stress- and defense-related genes in degenerating feeding cells.

Transcription profiling by array of soybean NIL-R vs NIL-S captured syncitia after infection with soybean cyst nematode

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