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6e9be818-55dd-4861-a525-70d1208e543b - samples

ABSTRACT: In this study we employed Laser Capture Microdissection (LCM) for the multimodal profiling of lung macrophages cell populations as a function of location within the healthy tissue. In detail, macrophage mini-bulks (~100 cells) were collected from 4 healthy human donors in 5 different locations of the airways (a total of 20 biopsies), including parenchyma (L1 Ã¢Â€Â“ lower left lobe (LLL); L6 Ã¢Â€Â“ 80% distance from LLL tip), trachea (L2), bronchi (L3 Ã¢Â€Â“ 1st/2nd generation; L5 Ã¢Â€Â“ 3rd/4th generation), and processed for ATAC-seq.

PROVIDER: EGAD00001008693 | EGA |

REPOSITORIES: EGA

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2aae4328-f515-4c3e-9f87-9142bf11f85b - samples

Project description:In the reported study, we employed Laser Capture Microdissection (LCM) for the transcriptome profiling of lung macrophages cells populations as a function of location within the healthy tissue. In detail, macrophage mini-bulks (100 cells each) were collected by LCM from 4 healthy human donors in 5 different locations of the airways (a total of 20 biopsies), including parenchyma (L1 Ã¢Â€Â“ lower left lobe (LLL); L6 Ã¢Â€Â“ 80% distance from LLL tip), trachea (L2), bronchi (L3 Ã¢Â€Â“ 1st/2nd generation; L5 Ã¢Â€Â“ 3rd/4th generation) and processed for RNA-seq.

| EGAD00001008694 | EGA

LCM-RNAseq on human lung macrophages

| EGAS00001006168 | EGA

LCM-ATACseq on human lung macrophages

Project description:In this study we employed Laser Capture Microdissection (LCM) for the multimodal profiling of lung macrophages cell populations as a function of location within the healthy tissue. In detail, macrophage mini-bulks (~100 cells) were collected from 4 healthy human donors in 5 different locations of the airways (a total of 20 biopsies), including parenchyma (L1 Ã¢Â€Â“ lower left lobe (LLL); L6 Ã¢Â€Â“ 80% distance from LLL tip), trachea (L2), bronchi (L3 Ã¢Â€Â“ 1st/2nd generation; L5 Ã¢Â€Â“ 3rd/4th generation), and processed for ATAC-seq.

| EGAS00001006167 | EGA

Quantitative and dynamic catalogs of proteins released during apoptotic and necroptotic cell death

Project description:The inflammatory functions of the cytokine tumor necrosis factor (TNF) rely on its ability to induce cytokine production and to induce cell death. Caspase dependent and independent pathways Ã¢â‚¬â€œ apoptosis and necroptosis Ã¢â‚¬â€œ respectively, regulate immunogenicity by the release of distinct sets of cellular proteins. To obtain an unbiased, systems-level understanding of this important process, we here applied mass spectrometry-based proteomics to dissect protein release during apoptosis and necroptosis. We report hundreds of proteins released from human myeloid cells in time-course experiments. Both cell death types induce receptor shedding, but only apoptotic cells released nucleosome components. Conversely, necroptotic cells release lysosomal components by activating lysosomal exocytosis at early stages of necroptosis- induced membrane permeabilisation and show reduced release of conventionally secreted cytokines.

2020-07-18 | PXD014966 | Pride

Early stages of yeast senescent cells

Project description:We performed transcriptional and metabolic profiling for yeast at early stages of senescence (4th, 7th and 11th generation), that is, for populations in which most cells are still alive. Transcriptional profiles showed up- and down-regulation for about 20% of the genes profiled after the first 4 generations, few further changes by the 7th generation, and an additional 12% of the genes were up- and down-regulated after 11 generations. Pathway analysis revealed that these 11th generation cells had accumulated transcripts coding for enzymes involved in sugar metabolism, the tricarboxylic acid (TCA) cycle and amino acid degradation, and showed decreased levels of mRNAs coding for enzymes involved in amino acid biosynthetic pathways. Stationary phase-induced genes were highly expressed after 11 generations even though the growth medium contained adequate levels of nutrients, indicating deterioration of the nutrient sensing and/or signaling pathways by the 11th generation. These changes are presumably early indications of replicative senescence. Cells of yeast strain BY4742 were labeled with biotin and cultivated in YPD medium at 30M-BM-0C. The labeled cells at early stages of senescence (4th, 7th and 11th generation) were isolated using Dynabeads Biotin Binder (Invitrogen, Carlsbad, CA, USA). Total RNA samples were prepared from the senescent cells. Antisense RNA was synthesized and labeled with Cy3 for the 4th, 7th, and 11th generation and with Cy5 for the 1st generation. Each mixture of Cy3- and Cy5-labeled antisense RNA was hybridized on a 3D-Gene Yeast Oligo Chip 6K (Toray, Kanagawa, Japan). The hybridized array was scanned with a 3D-Gene Scanner 3000 (Toray).

2014-07-27 | E-GEOD-59797 | biostudies-arrayexpress

Polyhexamethylene guanidine aerosol causes irreversible changes in blood proteins that associated with the severity of lung injury

Project description:Humidifier disinfectant (HD)-associated lung injury (HDLI) not only associates with increased acute morbidity and mortality, but also affects long term lung function due to lung fibrosis. However, there have been no validated marker capable of detecting exposure to HDs or severity of HDLI. This study aims to discover the differential abundant plasma proteome between them and develop prediction score platform using plasma proteome data from HD-exposed patients in order to classify the severity of HDLI. A total of 483 samples were used in this study. The samples used were 162 children in the normal group, 76 in the 4th stage, 51 in the 3rd stage, 54 in the 2nd stage, 42 in the 1st stage and 50 female adults in the normal group, 20 in the 4th stage, 7 in the 3rd stage, 6 in the 2nd stage, and 14 in 1st stage. The lower the grade, the greater the severity of HDLI.

2024-08-14 | PXD040122 | Pride

Expression and differential expression analysis of milk samples from healthy and diseased diary cows.

Project description:Expression and differential expression analysis of milk samples from healthy and diseased diary cows. Diseases were grouped by their occurrence in the mammary gland or extra-mammary. Furthermore, the diseases were classified by their severity. All cows were examined thoroughly by the dairy herd manager, trained staff, or a veterinarian. Expression and differential expression was assessed by using the Affymetrix Bovine Genome Array (GPL2112). Control animals (2-4 years old, 1st to 3th lactation, one animal 4th and one 8th lactation) showed no clinical signs of disease and had no abnormalities in the udder or milk. Their somatic cell count (SCC) was less than 100,000 cells/ml milk. Most of the control samples were taken during early lactation (10-100 days post-partum, dpp). Diseased cows were in their 1st to 8th lactation within 10-220 dpp.

2018-06-29 | GSE93082 | GEO

An automated and fast sample preparation workflow for laser microdissection guided ultrasensitive proteomics

Project description:Spatial tissue proteomics integrating whole-slide imaging, laser microdissection and ultrasensitive mass spectrometry is a powerful approach to link cellular phenotypes to functional proteome states in (patho)physiology. To be applicable to large patient cohorts and low sample input amounts, including single-cell applications, loss-minimized and streamlined end-to-end workflows are key. We here introduce an automated sample preparation protocol for laser microdissected samples utilizing the cellenONEÃ‚Â® robotic system, which has the capacity to process 192 samples in three hours. Following laser microdissection collection directly into the proteoCHIP LF 48 or EVO 96 chip, our optimized protocol facilitates lysis, formalin de-crosslinking and tryptic digest of low-input archival tissue samples. The seamless integration with the Evosep ONE LC system by centrifugation allows Ã¢â‚¬Ëœon-the-flyÃ¢â‚¬â„¢ sample clean-up, particularly pertinent for laser microdissected workflows. We validate our method in human tonsil archival tissue, where we profile proteomes of spatially-defined B-cell, T-cell and epithelial microregions of 4,000 Ã‚Âµm2 to a depth of ~2,000 proteins and with high cell type specificity. We finally provide detailed equipment templates and experimental guidelines for broad accessibility.

2024-03-22 | PXD047762 | Pride

Transcription regulation of sex-biased genes during ontogeny in the malaria vector Anopheles gambiae

Project description:Transcriptional analysis of sex-regulated genes from male and female dsxM-^VeGFP sexed larvae (1st instar, late 2nd /early 3rd instar and 4th instar), pupae and virgin non-blood-fed 3 day old adult A. gambiae mosquitoes

2011-05-01 | E-MEXP-3093 | biostudies-arrayexpress

Methylation Changes in Soybean Early Maturation Seed Compartments Using Laser Capture Microdissection (LCM)

Project description:What methylation changes are occurring in different compartments of early maturation stage seed largely remains unknown. To uncover the possible role of DNA methylation in different compartments of early maturation stage seed, we characterized the methylome of two major compartments (abaxial parenchyma and adaxial parenchyma) in embryonic cotyledon, four major compartments (parenchyma, plumule, root tip, and vascular) in embryonic axis, and seed coat layers (parenchyma and palisade) using Illumina sequencing. The whole seed coat and embryonic cotyledons were captured using LCM to serve as controls.

2012-05-11 | GSE37893 | GEO

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