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Expression data from Arabidopsis Seed Compartments at 5 discrete stages of development
Ryan Christopher Kirkbride, University of California, Department of Plant Biology, Davis, California (rkirkbride@ucdavis.edu,bobg@ucla.edu)
Experiment design (87 hybridizations)
developmental stage name
•globular stage •pre-globular stage •linear-cotyledon stage •heart stage •mature green stage •bending cotyledon stage
organism part name
•embryo proper •cellularized endosperm •micropylar endosperm •peripheral endosperm •chalazal endosperm •chalazal seed coat •seed coat •whole seeds •suspensor

This experiment has been imported by PLEXdb from NCBI GEO (GSE12404) Series_summary: This SuperSeries is composed of the following subset Seri...[complete overview]

Experiment     Expression     Hybridizations & Samples     Quality Control     Compare Treatments     Downloads    

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Experiment Name: Expression data from Arabidopsis Seed Compartments at 5 discrete stages of development
Accession No: AT107
Microarray: ATH1-121501
Visibility: public
Experiment Type:
Experiment Factor(s):
developmental stage name
•globular stage   •pre-globular stage   •linear-cotyledon stage   •heart stage   •mature green stage   •bending cotyledon stage
organism part name
•embryo proper   •cellularized endosperm   •micropylar endosperm   •peripheral endosperm   •chalazal endosperm   •chalazal seed coat   •seed coat   •whole seeds   •suspensor
Quality Control: biological replicates
Treatment summary:
 developmental stage name  organism part name  # replicates
 globular stage  embryo proper  2
 globular stage  cellularized endosperm  0
 globular stage  micropylar endosperm  2
 globular stage  peripheral endosperm  2
 globular stage  chalazal endosperm  3
 globular stage  chalazal seed coat  2
 globular stage  seed coat  2
 globular stage  whole seeds  2
 globular stage  suspensor  2
 pre-globular stage  embryo proper  2
 pre-globular stage  cellularized endosperm  0
 pre-globular stage  micropylar endosperm  2
 pre-globular stage  peripheral endosperm  2
 pre-globular stage  chalazal endosperm  2
 pre-globular stage  chalazal seed coat  2
 pre-globular stage  seed coat  2
 pre-globular stage  whole seeds  2
 pre-globular stage  suspensor  0
 linear-cotyledon stage  embryo proper  2
 linear-cotyledon stage  cellularized endosperm  2
 linear-cotyledon stage  micropylar endosperm  2
 linear-cotyledon stage  peripheral endosperm  0
 linear-cotyledon stage  chalazal endosperm  2
 linear-cotyledon stage  chalazal seed coat  2
 linear-cotyledon stage  seed coat  2
 linear-cotyledon stage  whole seeds  2
 linear-cotyledon stage  suspensor  0
 heart stage  embryo proper  2
 heart stage  cellularized endosperm  0
 heart stage  micropylar endosperm  2
 heart stage  peripheral endosperm  2
 heart stage  chalazal endosperm  3
 heart stage  chalazal seed coat  3
 heart stage  seed coat  2
 heart stage  whole seeds  2
 heart stage  suspensor  0
 mature green stage  embryo proper  2
 mature green stage  cellularized endosperm  0
 mature green stage  micropylar endosperm  2
 mature green stage  peripheral endosperm  2
 mature green stage  chalazal endosperm  2
 mature green stage  chalazal seed coat  2
 mature green stage  seed coat  2
 mature green stage  whole seeds  2
 mature green stage  suspensor  0
 bending cotyledon stage  embryo proper  2
 bending cotyledon stage  cellularized endosperm  0
 bending cotyledon stage  micropylar endosperm  0
 bending cotyledon stage  peripheral endosperm  2
 bending cotyledon stage  chalazal endosperm  2
 bending cotyledon stage  chalazal seed coat  2
 bending cotyledon stage  seed coat  2
 bending cotyledon stage  whole seeds  2
 bending cotyledon stage  suspensor  0
Total hybridizations: 87
Description: This experiment has been imported by PLEXdb from NCBI GEO (GSE12404)

Series_summary:
This SuperSeries is composed of the following subset Series:
GSE11262: Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage
GSE12402: Expression data from Arabidopsis seed compartments at the pre-globular stage
GSE12403: Expression data from Arabidopsis seed compartments at the linear-cotyledon stage
GSE15160: Expression data from Arabidopsis seed compartments at the heart stage
GSE15165: Expression data from Arabidopsis seed compartments at the mature green stage
GSE20039: Expression data from Arabidopsis seed compartments at the bending coyledon stage!Series_overall_design = Refer to individual Series

Series_overall_design:
Refer to individual Series

PLEXdb Curator's Note:
1. There are six developmental stages in this series although the title suggests 5. We have preserved the original title from GEO.

2. We have also made the following assumptions while deciding a factorial structure for this experiment:
a.
We have used ‘seed coat’ for all samples mentioning either ‘seed coat’ or ‘general seed coat’ (at GEO some sub-series have used ‘seed coat’ for heart and mature green stages and ‘general seed coat’ for the others).
b.
We have also used the term ‘whole seed’ for all samples that mention either ‘whole seed’ or ‘whole seed section’ because many of their descriptions contain ‘whole seed section’.
Publication: 'The seed composition of Arabidopsis mutants for the group 3 sulfate transporters indicates a role in sulfate translocation within developing seeds.', Hélène Zuber, Jean-Claude Davidian, Grégoire Aubert, Delphine Aimé, Maya Belghazi, Raphaël Lugan, Dimitri Heintz, Markus Wirtz, Rüdiger Hell, Richard Thompson and Karine Gallardo.
Plant Physiol 2010 Oct;154(2):913-26.
pubmed: 20702726
Created: 2011-02-17 12:26:38
Last Update: 2011-02-18 12:47:28
Released: 2011-02-25
GEO Accession GSE12404
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):
Homepage:

 
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