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Series GSE89100 Query DataSets for GSE89100
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
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.
 
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.
 
Contributor(s) Palovaara J
Citation(s) 29116234
Submission date Oct 24, 2016
Last update date Jan 15, 2018
Contact name Joakim Palovaara
E-mail(s) joakim@uni-bremen.de
Organization name Wageningen Univeristy
Department Biochemistry
Lab Dolf Weijers Lab
Street address Stippeneng 4
City Wageningen
State/province Gelderland
ZIP/Postal code 6708WE
Country Netherlands
 
Platforms (1)
GPL22599 [AraGene-1_1-st] Arabidopsis Gene 1.1 ST Array [CDF: aragene11st_At_TAIRG version 19]
Samples (38)
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]
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
Relations
BioProject PRJNA350282

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE89100_RAW.tar 193.7 Mb (http)(custom) TAR (of CEL)
Raw data provided as supplementary file
Processed data included within Sample table

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