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Series GSE89098 Query DataSets for GSE89098
Status Public on Nov 06, 2017
Title Nuclear and cellular expression data from the whole 16-cell stage Arabidopsis thaliana embryo
Organism Arabidopsis thaliana
Experiment type Expression profiling by array
Summary Due to its inaccessibility, transgenic methods have been recently developed to isolate tissue- or cell-specific nuclear RNA from the Arabidopsis embryo for transcriptomic profiling. While these approaches have made the it possible to conduct transcriptomic studies at the cellular level, only nuclear and not whole celluar RNA can be isolated. The question thus arrises if nuclear RNA is a reasonable proxy for whole cellular mRNA. To answer this, microarray-based transcriptomic profiling was used to determine genome-wide expression in nuclei and cells isolated from whole 16-cell stage Arabidopsis embryos.
Overall design We manually pollinated flowers and either isolated whole embryos (manually using an micromanipulator; cEMB) or the nuclei from embryos (using the INTACT method and a whole embryo marker; nEMB) at 16-cell stage (16C) of development (72h after pollination). Following RNA isolation, microarray-based transcriptomic profiling was performed on 3 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
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)
GPL22603 [AraGene-1_0-st] Arabidopsis Gene 1.0 ST Array [CDF: aragene10st_At_TAIRG version 19]
Samples (6)
GSM2358762 embryo, nuclei, biological replicate 1 [nEMB_16C1]
GSM2358763 embryo, nuclei, biological replicate 2 [nEMB_16C2]
GSM2358764 embryo, nuclei, biological replicate 3 [nEMB_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
BioProject PRJNA350284

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
GSE89098_RAW.tar 50.5 Mb (http)(custom) TAR (of CEL)
Raw data provided as supplementary file
Processed data included within Sample table

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