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Mouse lung and brain LCM-ATACseq

ABSTRACT: In situ transposition followed by laser capture microdissection was applied to lung and brain mouse tissue sections to demonstrate feasibility of LCM-based spatial chromatin accessibility analysis of regions of interest.

ORGANISM(S): Mus musculus

PROVIDER: GSE218216 | GEO | 2023/12/01

REPOSITORIES: GEO

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Mouse spleen LCM-ATACseq (B and T cell zones)

Project description:In situ transposition followed by laser capture microdissection was applied to spleen mouse tissue sections to demonstrate feasibility of LCM-based spatial chromatin accessibility analysis of regions of interest. B220 and CD3e immunostained B and T cell zones were analyzed.

2023-12-01 | GSE237824 | GEO

Tumor and stroma from breast by LCM

Project description:Tumor epithelium and surrounding stromal cells were isolated using laser capture microdissection of human breast cancer to examine differences in gene expression based on tissue types from inflammatory and non-inflammatory breast cancer Keywords: LCM

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Project description:The purpose of this study is to obtain comprehensive gene expression profiles in breast cancer. Mammary gland cells were specifically isolated from 433 clinical tissue samples by laser capture microdissection (LCM). Total RNAs were extracted from LCM captured samples. We investigated gene expression profiles in 417 patients with breast cancer and 16 non-tumor tissues as a normal control using an Affymetrix GeneChip.

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Laser Capture Microdissection (LCM) analysis of mycorrhizal rice roots

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Gene expression profiles of components isolated from developing kidney at E15.5 using LCM. (GUDMAP Series ID: 12)

Project description:The long term objective is to create an encyclopedia of the expression levels of all genes in multiple components of the developing kidney. The central thesis is straightforward. The combination of laser capture microdissection (LCM) plus microarray analysis offers a powerful, efficient and effective method for the creation of a global gene expression atlas of the developing kidney. Microarrays with essentially complete genome coverage can be used to quantitate expression levels of every gene in laser capture microdissected components of the developing kidney. The ensuing rapid read-out provides an expression atlas that is more sensitive, more economical and more complete than would be possible by in situ hybridizations alone. Keywords: Comparison of kidney components.

2006-12-23 | GSE6589 | GEO

Gene expression profiles of components isolated from developing kidney at E11.5, E12.5 & E15.5 using LCM. (GUDMAP Series ID: 10)

2006-11-18 | E-GEOD-6290 | biostudies-arrayexpress

LCM-Seq analysis of microscopically defined human embryo HSC microenvironment

Project description:This dataset contains RNA-Seq data for cells within spatially defined subdomains of the human embryo dorsal aorta, subdissected from tissue sections using laser capture microdissection. This dataset explores dorsal-ventral polarisation across the dorsal aorta, the site of hematopoietic stem cell emergence.

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Gene expression profiles of components isolated from developing kidney at E11.5, E12.5 & E15.5 using LCM. (GUDMAP Series ID: 10)

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Laser capture microdissection-capillary zone electrophoresis-tandem mass spectrometry (LCM-CZE-MS/MS) for spatially resolved top-down proteomics: a pilot study of zebrafish brain

Project description:Mass spectrometry (MS)-based spatially resolved top-down proteomics (TDP) of tissues is crucial for understanding the roles played by microenvironmental heterogeneity in the biological functions of organs and for discovering new proteoform biomarkers of diseases. There are few published spatially resolved TDP studies. One of the challenges relates to the limited performance of TDP for the analysis of spatially isolated samples using, for example, laser capture microdissection (LCM) because those samples are usually mass-limited. We present the first pilot study of LCM-capillary zone electrophoresis (CZE)-MS/MS for spatially resolved TDP and used zebrafish brain as the sample. The LCM-CZE-MS/MS platform employed a non-ionic detergent and a freeze-thaw method for efficient proteoform extraction from LCM isolated brain sections followed by CZE-MS/MS without any sample cleanup step, ensuring high sensitivity. Over 400 proteoforms were identified in a CZE-MS/MS analysis of one LCM brain section via consuming the protein content of roughly 250 cells. We observed drastic differences in proteoform profiles between two LCM brain sections isolated from the optic tectum (Teo) and telencephalon (Tel) regions. Proteoforms of three proteins (npy, penkb, and pyya) having neuropeptide hormone activity were exclusively identified in the isolated Tel section. Proteoforms of reticulon, myosin, and troponin were almost exclusively identified in the isolated Teo section, and those proteins play essential roles in visual and motor activities. The proteoform profiles accurately reflected the main biological functions of the Teo and Tel regions of the brain. Additionally, hundreds of post-translationally modified proteoforms were identified.

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Gene expression profiles of E15.5 cortical collecting duct and anlage of loop of Henle isolated from developing kidney using LCM. (GUDMAP Series ID: 18)

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