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Title: RNA sequencing of laser-capture microdissected compartments of the maize kernel identifies regulatory modules associated with endosperm cell differentiation      
dateReleased:
02-13-2015
description:
Endosperm is an absorptive structure that supports embryo development or seedling germination in angiosperms. The endosperm of cereals is a main source of food, feed, and industrial raw materials worldwide. However, the gene regulatory networks that control endosperm cell differentiation remain largely unclear. As a first step toward characterizing these networks, we profiled the mRNAs in five major cell types of the differentiating endosperm and in the embryo and four maternal compartments of the kernel. Comparisons of these mRNA populations revealed the diverged gene expression programs between filial and maternal compartments, and an unexpected close correlation between embryo and the aleurone layer of endosperm. Gene co-expression network analysis identified co-expression modules associated with single or multiple kernel compartments including modules for the endosperm cell types, some of which showed enrichment of previously identified temporally activated and/or imprinted genes. Detailed analyses of a co-expression module highly correlated with the basal endosperm transfer layer (BETL) identified a regulatory module activated by MRP-1, a regulator of BETL differentiation and function. These results provide a high-resolution atlas of gene activity in the compartments of the maize kernel and help to uncover the regulatory modules associated with the differentiation of the major endosperm cell types. RNAs from ten compartments of the maize kernel including the central starchy endosperm (CSE), conducting zone (CZ), aleurone (AL), basal endosperm transfer layer (BETL), embryo-surrounding region (ESR), nucellus (NU), pericarp (PE), placenta-chalazal region (PC), the vascular region of the pedicel (PED), and the embryo (EMB) were isolated at 8 days after pollination (DAP) using laser-capture microdissection and sequenced using an Illumina HiSeq 2000 platform.
privacy:
not applicable
aggregation:
instance of dataset
ID:
E-GEOD-62778
refinement:
raw
alternateIdentifiers:
62778
keywords:
functional genomics
dateModified:
04-12-2016
availability:
available
types:
gene expression
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-62778/E-GEOD-62778.raw.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-62778/E-GEOD-62778.processed.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62778
storedIn:
Gene Expression Omnibus
qualifier:
not compressed
format:
HTML
accessType:
landing page
primary:
true
authentication:
none
authorization:
none
abbreviation:
EBI
homePage: http://www.ebi.ac.uk/
ID:
SCR:004727
name:
European Bioinformatics Institute
homePage: https://www.ebi.ac.uk/arrayexpress/
ID:
SCR:002964
name:
ArrayExpress

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