Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

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Transcription profiling of Arabidopsis wild type and yda-2 mutant plants


ABSTRACT: Wild type and yda-2 plants were germinated and grown on commercial potting mix in walk-in chambers with constant illumination (~150 micromoles per square meter per second) at 22oC. The aerial parts of the plants were harvested at the rosette stage, prior to bolting. Total RNA was prepared using Trizol reagent (Invitrogen) with the additional steps recommended for polysaccharide-rich tissues. Hybridization probes for the GeneChip AtGenome1 microarrays (Affymetrix) were prepared from 20 mg total RNA. All procedures followed Affymetrix protocols. Briefly, cDNA was synthesized using Superscript reverse transcriptase (Invitrogen) and a T7-(dT)24 primer, purified by phenol/chloroform extraction using Phase Lock Gel tubes (Eppendorf), and precipitated with ethanol. Labeled antisense RNA was generated with a BioArray kit (Enzo) and purified using an RNeasy kit (Qiagen). 25 mg of the fragmented cRNAs were used for hybridization to the arrays. Affymetrix instruments were used for hybridization, washing, staining and scanning of the arrays according to the provided instructions. Data from four biological replications representing tissue grown and harvested at different times was collected. The average signals of all eight experiments were scaled to the target value of 500.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Chris Somerville 

PROVIDER: E-GEOD-919 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

A MAPKK kinase gene regulates extra-embryonic cell fate in Arabidopsis.

Lukowitz Wolfgang W   Roeder Adrienne A   Parmenter Dana D   Somerville Chris C  

Cell 20040101 1


The Arabidopsis zygote divides asymmetrically into an embryonic apical cell and a basal cell with mostly extra-embryonic fate. This fundamental asymmetry sets the stage for further embryonic development, but the events mediating it are poorly understood. We have identified a MAPKK kinase gene, named YODA, that promotes extra-embryonic cell fates in the basal lineage. In loss-of-function mutants, the zygote does not elongate properly, and the cells of the basal lineage are eventually incorporated  ...[more]

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