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| Status |
Public on Nov 06, 2017 |
| Title |
Cell type-specific expression atlas of the early Arabidopsis thaliana embryo |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Expression profiling by array
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| Summary |
The establishement of the first plant tissues occurs during embryo development. Indeed, cell types that will form the Arabidopsis root stem cell niche are first specified during 16-cell (16C), early globular (EG) and late globular (LG) stage of embryonic development. While some regulatory factors are known, we do not yet understand the genetic networks underlying the specification of these cell types. One main reason for this is the difficulties in adapting genome-wide approaches to the cellular level. Here, we have adapted such an approach (INTACT) to generate microarray-based cell type-specific transcriptomic profiles at 16C to LG stage for use in determining the role of the transcriptome in cell specification and differentiation during root stem cell niche formation.
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| Overall design |
We manually pollinated flowers and isolated cell type-specific nuclei from embryos using the INTACT method and cell type-specific markers at 16-cell stage (72h after pollination), EG stage (81h after pollination) and LG (100h after pollination) of development. Following RNA isolation, microarray-based transcriptomic profiling was performed on 3-4 pooled biological replicates each.
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| Contributor(s) |
Palovaara J |
| Citation(s) |
29116234 |
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| Submission date |
Oct 24, 2016 |
| Last update date |
Jan 15, 2018 |
| Contact name |
Joakim Palovaara |
| E-mail(s) |
joakim@uni-bremen.de
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| Organization name |
Wageningen Univeristy
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| Department |
Biochemistry
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| Lab |
Dolf Weijers Lab
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| Street address |
Stippeneng 4
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| City |
Wageningen |
| State/province |
Gelderland |
| ZIP/Postal code |
6708WE |
| Country |
Netherlands |
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| Platforms (1) |
| GPL22599 |
[AraGene-1_1-st] Arabidopsis Gene 1.1 ST Array [CDF: aragene11st_At_TAIRG version 19] |
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| Samples (38)
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| GSM2358788 |
16-cell_inner lower tier, nuclei, biological replicate 1 [nILT_16C1] |
| GSM2358789 |
16-cell_inner lower tier, nuclei, biological replicate 2 [nILT_16C2] |
| GSM2358790 |
16-cell_inner lower tier, nuclei, biological replicate 3 [nILT_16C3] |
| GSM2358791 |
16-cell_embryo, nuclei biological replicate 1 [nEMB_16C1] |
| GSM2358792 |
16-cell_embryo, nuclei biological replicate 2 [nEMB_16C2] |
| GSM2358793 |
16-cell_embryo, nuclei biological replicate 3 [nEMB_16C3] |
| GSM2358794 |
Early globular (EG)_vascular, nuclei biological replicate 1 [nVSC_EG1] |
| GSM2358795 |
Early globular (EG)_vascular, nuclei biological replicate 2 [nVSC_EG2] |
| GSM2358796 |
Early globular (EG)_vascular, nuclei biological replicate 3 [nVSC_EG3] |
| GSM2358797 |
Early globular (EG)_vascular, nuclei biological replicate 4 [nVSC_EG4] |
| GSM2358798 |
Early globular (EG)_ground tissue, nuclei, biological replicate 1 [nGSC_EG1] |
| GSM2358799 |
Early globular (EG)_ground tissue, nuclei, biological replicate 2 [nGSC_EG2] |
| GSM2358800 |
Early globular (EG)_ground tissue, nuclei, biological replicate 3 [nGSC_EG3] |
| GSM2358801 |
Early globular (EG)_ground tissue, nuclei, biological replicate 4 [nGSC_EG4] |
| GSM2358802 |
Early globular (EG)_suspensor, nuclei, biological replicate 1 [nSUS_EG1] |
| GSM2358803 |
Early globular (EG)_suspensor, nuclei, biological replicate 2 [nSUS_EG2] |
| GSM2358804 |
Early globular (EG)_suspensor, nuclei, biological replicate 3 [nSUS_EG3] |
| GSM2358805 |
Early globular (EG)_embryo, nuclei, biological replicate 1 [nEMB_EG1] |
| GSM2358806 |
Early globular (EG)_embryo, nuclei, biological replicate 2 [nEMB_EG2] |
| GSM2358807 |
Early globular (EG)_embryo, nuclei, biological replicate 3 [nEMB_EG3] |
| GSM2358808 |
Early globular (EG)_embryo, nuclei, biological replicate 4 [nEMB_EG4] |
| GSM2358809 |
Late globular (LG)_vascular, nuclei, biological replicate 1 [nVSC_LG1] |
| GSM2358810 |
Late globular (LG)_vascular, nuclei, biological replicate 2 [nVSC_LG2] |
| GSM2358811 |
Late globular (LG)_vascular, nuclei, biological replicate 3 [nVSC_LG3] |
| GSM2358812 |
Late globular (LG)_vascular, nuclei, biological replicate 4 [nVSC_LG4] |
| GSM2358813 |
Late globular (LG)_ground tissue, nuclei, biological replicate 1 [nGSC_LG1] |
| GSM2358814 |
Late globular (LG)_ground tissue, nuclei, biological replicate 2 [nGSC_LG2] |
| GSM2358815 |
Late globular (LG)_ground tissue, nuclei, biological replicate 3 [nGSC_LG3] |
| GSM2358816 |
Late globular (LG)_suspensor, nuclei, biological replicate 1 [nSUS_LG1] |
| GSM2358817 |
Late globular (LG)_suspensor, nuclei, biological replicate 2 [nSUS_LG2] |
| GSM2358818 |
Late globular (LG)_suspensor, nuclei, biological replicate 3 [nSUS_LG3] |
| GSM2358819 |
Late globular (LG)_QC, nuclei, biological replicate 1 [nQC_LG1] |
| GSM2358820 |
Late globular (LG)_QC, nuclei, biological replicate 2 [nQC_LG2] |
| GSM2358821 |
Late globular (LG)_QC, nuclei, biological replicate 3 [nQC_LG3] |
| GSM2358822 |
Late globular (LG)_embryo, nuclei biological replicate 1 [nEMB_LG1] |
| GSM2358823 |
Late globular (LG)_embryo, nuclei biological replicate 2 [nEMB_LG2] |
| GSM2358824 |
Late globular (LG)_embryo, nuclei biological replicate 3 [nEMB_LG3] |
| GSM2358825 |
Late globular (LG)_embryo, nuclei biological replicate 4 [nEMB_LG4] |
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| This SubSeries is part of SuperSeries: |
| GSE89101 |
Nuclear and cellular expression data from the whole 16-cell stage Arabidopsis thaliana embryo and a cell type-specific expression atlas of the early Arabidopsis embryo |
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| Relations |
| BioProject |
PRJNA350282 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE89100_RAW.tar |
193.7 Mb |
(http)(custom) |
TAR (of CEL) |
| Processed data included within Sample table |
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