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Expression data from Arabidopsis seed compartments at the pre-globular stage
Ryan Christopher Kirkbride, University of California, Department of Plant Biology, Davis, California (rkirkbride@ucdavis.edu,bobg@ucla.edu)
Experiment design (14 hybridizations)
organism part name
•embryo proper •micropylar endosperm •peripheral endosperm •chalazal endosperm •chalazal seed coat •general seed coat •whole seed sections

This experiment has been imported by PLEXdb from NCBI GEO (GSE12402) Series_summary: We collected pre-globular stage seed compartments from 7-m...[complete overview]

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Experiment Name: Expression data from Arabidopsis seed compartments at the pre-globular stage
Accession No: AT102
Microarray: ATH1-121501
Visibility: public
Experiment Type:
Experiment Factor(s):
organism part name
•embryo proper   •micropylar endosperm   •peripheral endosperm   •chalazal endosperm   •chalazal seed coat   •general seed coat   •whole seed sections
Quality Control: biological replicates
Treatment summary:
 organism part name  # replicates
 embryo proper  2
 micropylar endosperm  2
 peripheral endosperm  2
 chalazal endosperm  2
 chalazal seed coat  2
 general seed coat  2
 whole seed sections  2
Total hybridizations: 14
Description: This experiment has been imported by PLEXdb from NCBI GEO (GSE12402)

Series_summary:
We collected pre-globular stage seed compartments from 7-micron paraffin sections using the Leica LMD6000 system in order to identify the mRNAs present in different compartments of seeds containing pre-globular-stage embryos was identified as those seeds containing embryo propers made up of between 2 and 8 cells. For the purposes of this study we captured 6 compartments: embyro proper, micropylar endosperm, peripheral endosperm, chalazal endosperm, chalazal seed coat and general seed coat. Serial sections of entire seeds were also captured for comparison.

Keywords: cell type comparison

Series_overall_design:
Pre-globular stage seed compartments or whole seeds were isolated using the LMD6000 system. Total RNA was amplified and hybridized with Affymetrix ATH1 Arabidopsis array for 14 samples (embryo proper, micropylar endosperm, peripheral endosperm, chalazal endosperm, general seed coat, chalazal seed coat, whole seeds, 2 biological replicates each).

PLEXdb Curator's Note
This sub-series is part of the super-series GSE12404 (Expression Data from Arabidopsis Seed Compartments at 5 Discrete Stages of Development); the sister series are GSE11262 (globular stage), GSE12403 (linear-cotyledon stage), GSE15160 (Heart Stage), GSE15165 (mature green stage), and GSE20039 (bending cotyledon stage).
Publication: 'Global analysis of gene activity during Arabidopsis seed development and identification of seed-specific transcription factors.', Le BH, Cheng C, Bui AQ, Wagmaister JA, Henry KF, Pelletier J, Kwong L, Belmonte M, Kirkbride R, Horvath S, Drews GN, Fischer RL, Okamuro JK, Harada JJ, Goldberg RB.
Proc Natl Acad Sci U S A 2010 May 4;107(18):8063-70.
pubmed: 20385809
Created: 2011-02-15 11:25:39
Last Update: 2011-02-15 12:30:04
Released: 2011-02-24
GEO Accession GSE12402
Submitter: PLEXdb Curator
Name: Ryan Christopher Kirkbride
Institution: University of California, Department of Plant Biology, Davis, California
Head of Laboratory: Robert B. Goldberg
email(s):
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