Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Multi-omics reveals changes in astrocyte fatty acid metabolism during early stages of Alzheimer's disease

ABSTRACT: Protein from astrocytes of 6-month-old AD and WT mice (n=3) was extracted and digested using the iST kit (PreOmics) following the manufacturer's protocol. For label-free LC-MS analysis, samples were loaded onto a 25 cm C18 analytical column (Ionopticks) at a flow rate of 300 nL/min and subjected to gradient elution using solvents A (H2O-FA, 99.9:0.1 v/v) and B (ACN-FA, 99.9:0.1 v/v).For the database search conducted using MaxQuant, utilizing the Andromeda search engine for label-free quantification (LFQ) analysis.

ORGANISM(S): Mus Musculus

SUBMITTER: Jun Wan

PROVIDER: PXD054941 | iProX | Fri Aug 16 00:00:00 BST 2024

REPOSITORIES: iProX

ACCESS DATA

Json Xml

Similar Datasets

Assessment and Evaluation of Contemporary Approaches for Astrocyte Differentiation from hiPSCs: A Modeling Paradigm for Alzheimer's Disease

Project description:Background: Astrocytes have recently gained attention as key players in the pathogenesis of neurodegenerative diseases, including Alzheimer's disease. Numerous differentiation protocols have been developed to study human astrocytes in vitro. However, the properties of the resulting glia are inconsistent, making it difficult to select an appropriate method for a given research question. Therefore, we compared three approaches for the generation of iPSC-derived astrocytes. We performed a detailed analysis using a widely used long serum-free (LSFP) and short serum-free (SSFP) protocol, as well as a TUSP protocol using serum for a limited time of differentiation. Results: We used RNA sequencing and immunochemistry to characterize the cultures. Astrocytes generated by the LSFP and SSFP methods differed significantly in their characteristics from those generated by the TUSP method using serum. The TUSP astrocytes had a less neuronal pattern, showed a higher degree of extracellular matrix formation, and were more mature. The short-term presence of FBS in the medium facilitated the induction of astroglia characteristics but did not result in reactive astrocytes. Data from cell-type deconvolution analysis applied to bulk transcriptomes from the cultures assessed their similarity to primary and fetal human astrocytes. Conclusions: Overall, our analyses highlight the need to consider the advantages and disadvantages of a given differentiation protocol for solving specific research tasks or drug discovery studies with iPSC-derived astrocytes.

2024-10-15 | GSE269743 | GEO

Studying heterogeneity in embryonic stem cells using the approach of search-engine

Project description:Here we designed a search-engine for single-cell epigenome profiles. We tested different application of search-engine using different data-sets including mESC scATAC-seq profile.

2022-12-27 | GSE192644 | GEO

RNA-seq for understanding effects of vitamin B12 removal on astrocyte culture

Project description:Astrocytes express a vitamin B12 uptake receptor, CD320/TCblR, that is regulated by S1P1 signaling. In search of genes controlled under B12 deficiency in astrocytes, we employed RNA-seq using RNA of astrocytes cultured in normal or B12 deficient media.

2022-05-17 | GSE99113 | GEO

Genome wide expression analysis of BMP and LIF induce astrocyte differentiaion of mouse neural stem cells

Project description:Astrocytes perform a wide array of physiological functions. Despite the well-known functional and morphological diversity of astrocytes, molecular markers that label sub populations of astrocytes are limited. BMP and LIF are known to generated astrocytes with different morphology and physiological properties. The goal of this study to identify genes that are differentially expressed in BMP and LIF generated astrocytes.

2015-10-01 | GSE67942 | GEO

Astrocyte SplitBioID LFQ Proteomics

Project description:LC-MS/MS analysis of Split-BirA expressed in mouse Astrocytes. Data aquired on a Fusion Lumos and subjected to label-free relative quantitation withing Protein Discoverer (v 4.2). Sample key; Split-TuboID (47826, 47827, 47825) soluble TurboID (47838, 47839, 47840) TurboID-surface (TurboID-GPI; 47833, 47834, 47835)

2020-07-23 | MSV000085821 | MassIVE

Microarray analysis of the astrocyte transcriptome in the ageing brain: relationship to Alzheimer's pathology and ApoE genotype

Project description:Astrocyte dysfunction impacts their normal function, including neuronal support, thereby contributing to neurodegenerative pathologies including Alzheimer's disease (AD). Therefore to understand the role of astrocytes in the pathogenesis of age-related disorders we analysed the gene expression profile of astrocytes with respect to Alzheimer-type pathology. The aim of the present study was to combine immuno-LCM and microarray analysis to characterise the astrocyte transcriptome at different Braak stages, and with respect to ApoE genotype, in post-mortem human temporal cortex sampled dervied from the Medical Research Council Cognitive Function and Ageing Study (MRC-CFAS). GFAP-positive astrocytes were isolated from age, sex and brain pH-matched cases derived from the MRC-CFAS cohort, using immuno laser capture microdissection. The extracted RNA was amplified and applied to HGU133 Plus 2.0 Affymetrix gene arrays. Genes were considered differentially expressed if they showed a minimum 1.5 fold change at p<0.02 in all 6 individual cases in each stage of pathology [18 cases in total: 6 cases Braak stages I-II (3 cases carried at least one ApoE epsilon4 allele and 3 were ApoEe4 negative); 6 cases Braak stages III-IV (3 ApoEe4 positive and 3 ApoEe4 negative; 6 cases Braak stages V-VI (3 ApoEe4 positive and 3 ApoEe4 negative)]. keywords: human GFAP-positive astrocytes

2011-06-01 | E-GEOD-29652 | biostudies-arrayexpress

Tina Maio-Tracey Rouault Nsp12 data

Project description:Label free quantitation of 10 samples. Data acquisition was performed on UltiMate 3000 RSLC/Orbitrap Fusion Lumos system. The database search was performed with Proteome Discoverer 2.4 using SequestHT as search engine.

2021-05-02 | MSV000087353 | MassIVE

Tal Keren Kaplan and Juan Bonifacino LFQ data

Project description:Label free quantitation of 15 samples. Data acquisition was performed on UltiMate 3000 RSLC/Orbitrap Fusion Lumos system. The database search was performed with Proteome Discoverer 2.4 using SequestHT as search engine.

2021-06-30 | MSV000087730 | MassIVE

Tal Keren Kaplan and Juan Bonifacino LFQ data Sprot-Huamn-Cano

2021-07-01 | MSV000087741 | MassIVE

Studying heterogeneity in embryonic stem cells using the approach of search-engine

Project description:Studying heterogeneity in embryonic stem cells using the approach of search-engine

| PRJNA792553 | ENA