Project description:We used laser capture microdissection (LCM) to capture globular stage common bean embryo proper and suspensor, and profiled the transcriptome of these two embryo regions using next-generation sequencing. Our long-term goal is to understand the region-specific differentiation processes that occur during early embryo development and how genes are activated specifically in the suspensor and embryo proper. Illumina sequencing of transcripts from laser-captured embryo proper and suspensor regions of common bean globular stage embryo. Two biological replicates were collected for each embryo region.

2014-05-10 | E-GEOD-57535 | biostudies-arrayexpress

Transcript Profiling of Scarlet Runner Bean Embryo Regions at Globular Stage Using Laser Capture Microdissection Coupled with RNA-Seq

Project description:We used laser capture microdissection (LCM) to capture globular scarlet runner bean embryo propers and suspensors, and profiled the transcriptomes of these two embryo regions using next-generation sequencing. Our long-term goal is to understand the region-specific differentiation processes that occur during early embryo development and how genes are activated specifically in the suspensor and embryo proper. Illumina sequencing of transcripts from laser-captured embryo proper and suspensor regions of scarlet runner bean globular stage embryos. Two biological replicates were collected for each embryo region.

2014-05-10 | E-GEOD-57536 | biostudies-arrayexpress

Transcript Profiling of Phaseolus coccineus and Phaseolus vulgaris Embryo Regions at Globular Stage Using Laser Capture Microdissection Coupled with RNA-Seq

Project description:Transcript Profiling of Phaseolus coccineus and Phaseolus vulgaris Embryo Regions at Globular Stage Using Laser Capture Microdissection Coupled with RNA-Seq

| PRJNA246608 | ENA

Transcript Profiling of Soybean Seed Compartments Using Laser Capture Microdissection Coupled With RNA-Seq

2011-05-10 | GSE29162 | GEO

Transcript Profiling of Soybean Seed Compartments Using Laser Capture Microdissection Coupled With RNA-Seq

Project description:We used laser capture microdissection (LCM) to capture soybean seed compartments and profiled the transcriptomes of several compartments using next-generation sequencing. We profiled the transcriptomes of the embryo-proper and the suspensor region from globular stage embryos and the seed coat parenchyma layer of early maturation stage seeds using the Illumina GAIIx system. Illumina sequencing of transcripts from laser-captured embryo proper and suspensor of globular stage embryo and seed coat parenchyma layer of the early maturation stage seed.

2011-05-10 | E-GEOD-29162 | biostudies-arrayexpress

Combined use of laser capture microdissection and cDNA microarray analysis identifies locally expressed disease-related genes in focal regions of psoriasis vulgaris skin lesions.

Project description:Psoriasis vulgaris is a complex disease characterized by alterations in growth and differentiation of epidermal keratinocytes, as well as a marked increase in leukocyte populations. Lesions are known to contain alterations in messenger RNAs encoding more than 1,000 products, but only a very small number of these transcripts has been localized to specific cell types or skin regions. In this study, we used laser capture microdissection (LCM) and gene array analysis to study the gene expression of cells in lesional epidermis (EPI) and dermis, compared with the corresponding non-lesional regions. Using this approach, we detected >1,800 differentially expressed gene products in the EPI or dermis of psoriasis lesions. These results established sets of genes that are differentially expressed between epidermal and dermal compartments, as well as between non-lesional and lesional psoriasis skin. One of our findings involved the local production of CCL19, a lymphoid-organizing chemokine, and its receptor CCR7 in psoriatic dermal aggregates, along with the presence of gene products LAMP3/DC-LAMP and CD83, which typify mature dendritic cells (DCs). Gene expression patterns obtained with LCM and microarray analysis along with T-cell and DC detection by immune staining suggest a possible mechanism for lymphoid organization via CCL19/CCR7 in diseased skin.

| S-EPMC3352975 | biostudies-literature

Phosphorylation of TIP3 Aquaporins during Phaseolus vulgaris Embryo Development.

Project description:The membrane phosphoproteome in plant seed changes dynamically during embryo development. We examined the patterns of Phaseolus vulgaris (common bean) seed membrane protein phosphorylation from the mid-maturation stage until two days after germination. Serine and threonine phosphorylation declined during seed maturation while tyrosine phosphorylation remained relatively constant. We discovered that the aquaporin PvTIP3;1 is the primary seed membrane phosphoprotein, and PvTIP3;2 shows a very low level of expression. The level of phosphorylated Ser7 in PvTIP3;1 increased four-fold after seed maturation. Since phosphorylation increases water channel activity, we infer that water transport by PvTIP3;1 is highest in dry and germinating seeds, which would be optimal for seed imbibition. By the use of isoform-specific, polyclonal peptide antibodies, we found that PvTIP3;2 is expressed in a developmental pattern similar to PvTIP3;1. Unexpectedly, PvTIP3;2 is tyrosine phosphorylated following seed maturation, which may suggest a mechanism for the regulation of PvTIP3;2 following seed germination. Analysis of protein secondary structure by circular dichroism spectroscopy indicated that the amino-terminal domain of PvTIP3;1 is generally unstructured, and phosphorylation increases polyproline II (PPII) helical structure. The carboxy-terminal domain also gains PPII character, but in a pH-dependent manner. These structural changes are a first step to understand TIP3 aquaporin regulation.

| S-EPMC6912600 | biostudies-literature

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