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E-GEOD-62778

ABSTRACT: RNA sequencing of laser-capture microdissected compartments of the maize kernel identifies regulatory modules associated with endosperm cell differentiation

OTHER RELATED OMICS DATASETS IN: PRJNA265095

PROVIDER: E-GEOD-62778 | ExpressionAtlas | 2019-05-15

REPOSITORIES: ExpressionAtlas

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			Action	DRS
	E-GEOD-62778-analysis-methods.tsv	Tabular
	E-GEOD-62778-atlasExperimentSummary.Rdata	Rdata
	E-GEOD-62778-coexpressions.tsv.gz	Tabular
	E-GEOD-62778-configuration.xml	Xml
	E-GEOD-62778-factors.xml	Xml

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E-GEOD-61057

Project description:Transcription profiling by high throughput sequencing of aleurone and starchy endosperm cells were isolated by laser-capture microdissection in maize nkd mutants

2019-05-14 | E-GEOD-61057 | ExpressionAtlas

RNA sequencing of laser-capture microdissected compartments of the maize kernel identifies regulatory modules associated with endosperm cell differentiation

Project 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.

2015-02-13 | E-GEOD-62778 | biostudies-arrayexpress

E-GEOD-26866

Project description:Combined Use of Laser Capture Microdissection and Microarray Analysis Identifies Locally Expressed Disease-Related Genes in Focal Regions of Psoriasis Vulgaris Skin Lesions

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The naked endosperm genes encode duplicate ID domain transcription factors required for maize endosperm differentiation

Project description:The objective of the current study is to unravel the gene regulatory networks controlled by the nkd genes during maize endosperm developent. We compared wild type (B73) vs. nkd mutant (introgressed into B73 background) transcriptomes in aleurone vs. starchy endosperm cell types captured by laser capture microdissection technology.

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Identification of temporal regulatory modules associated with proliferation and differentiation in early maize endosperm development

Project description:Endosperm is a product of double fertilization and functions as a nutritive tissue in the angiosperm seed to support the growth of the embryo or the germinating seedling. In cereal grains, endosperm comprises a large proportion of the mature seed and contains large amounts of carbohydrates and proteins. To identify a high-resolution temporal transcriptome of the earliest stages of endosperm development, we used laser-capture microdissection to isolate and profile mRNA populations of a developmental series of the endosperm from 0 to 4 DAP in maize inbred B73. These stages comprise the initial period of proliferation of the triploid endosperm coenocyte through cellularized endosperm that shows an overall polarity and indications of early cell differentiation. Using computational tools, we identified distinct temporal co-expression modules during this period of development. Analysis of the co-expressed transcription-factor genes and the associated cis-regulatory elements allowed us to hypothesize gene regulatory networks involved in early endosperm development in maize.

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RNA-Seq Analysis of Laser-Capture Microdissected Cells of the Developing Central Starchy Endosperm of Maize

Project description:Endosperm is a product of double fertilization, and provides nutrients and signals to the embryo during seed development in flowering plants. Early stages of endosperm development are critical for the development of its storage capacity through synthesis and accumulation of starch and storage proteins. Here we report on the isolation and sequencing of mRNAs from the central portion of the starchy endosperm of Zea mays (maize) B73 at 6 days after pollination. We detected high correlation among the four biological replicates of RNAs isolated using laser-capture microdissection of the cell type. Because the assayed stage of development precedes the synthesis and accumulation of the major storage proteins and starch in the endosperm, our dataset likely include mRNAs for genes that are involved in control and establishment of these developmental programs. Four replicates of mRNAs from the central portion of starchy endopserm were isolated using laser-capture microdissection and sequenced using the Illumina GAIIx platform.

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E-MTAB-4395

Project description:Transcription profiling by high throughput sequencing of maize embryo and endosperm during development

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E-GEOD-44651

Project description:Laser Capture Microdissection isolation of preovulatory granulosa cells from WT and bERKO ovaries

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The naked endosperm genes encode duplicate ID domain transcription factors required for maize endosperm differentiation

Project description:The objective of the current study is to unravel the gene regulatory networks controlled by the nkd genes during maize endosperm development. We compared wild type (B73) vs. nkd mutant (introgressed into B73 background) transcriptomes in aleurone vs. starchy endosperm cell types captured by laser capture microdissection technology. We performed RNA seq analysis of mid-mature (15DAP) endosperm in two cell types [aleurone (A) and starchy endosperm (S)] of wild type B73 (B) and nkd mutant (N) kernels with three independent biological replicates.

2015-01-28 | E-GEOD-61057 | biostudies-arrayexpress

RNA-Seq Analysis of Laser-Capture Microdissected Cells of the Developing Central Starchy Endosperm of Maize

2014-06-17 | GSE58504 | GEO