Integrating single-cell and spatially resolved transcriptomic strategies to survey astrocytes in response to stroke
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Q Exactive HF-X
ORGANISM(S): Mus Musculus (mouse)
TISSUE(S): Brain
SUBMITTER: 
Jiaxi Peng
LAB HEAD: Aaron R. Wheeler
PROVIDER: PXD041388 | Pride | 2024-04-16
REPOSITORIES: Pride
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SC20220218D10_1.raw | Raw | |||
| SC20220218D10_10.raw | Raw | |||
| SC20220218D10_11.raw | Raw | |||
| SC20220218D10_12.raw | Raw | |||
| SC20220218D10_13.raw | Raw |
Items per page: 5 1 - 5 of 39 |
Similar Datasets
Project description:Dimethyl labeling was integrated into the microfluidic pipeline to allow for precise relative quantification of the trace samples at the nanogram level, and the new pipeline was applied to evaluating cancer cell lines and cancer tissue samples.
2023-03-24 | PXD036982 | Pride
Project description:To correlate gene expression profiles to fundamental biological processes such as cell growth, differentiation and migration, it is essential to work at the single cell level. Gene expression analysis always starts with the relatively low efficient reverse transcription (RT) of RNA into complementary DNA (cDNA), an essential step as unprocessed RNAs will not be analyzed further. In this paper, we present a novel method for RT that uses microfluidics to manipulate nanoliter volumes. We compare our method to conventional protocols performed in microliter volumes. More specifically, reverse transcription was performed either in a poly-dimethylsiloxane (PDMS) rotary mixer or in a tube, using single cell amount of mouse brain RNA (10 pg), and was followed by a template-switching PCR (TS-PCR) amplification step. We demonstrate that, using the microfluidic protocol, 74% of the genes expressed in mouse brain were detected, while only 4% were found with the conventional approach. We next profiled single neuronal progenitors. Using our microfluidic approach, i.e. performing cell capture, lysis and reverse transcription on-chip followed by TS-PCR amplification in tube, a mean of 5000 genes were detected in each neuron, which corresponds to the expected number of genes expressed in a single cell. This demonstrates the outstanding sensitivity of the microfluidic method. Keywords: Single cell, transcriptome, PDMS, microfluidic, reverse-transcription (RT), template-switching, lab-on-a-chip
2008-02-15 | GSE6941 | GEO
Project description:Joint profiling of chromatin accessibility and gene expression from the same single cell provides critical information about cell types in a tissue and cell states during a dynamic process. These emerging multi-omics techniques help the investigation of cell-type resolved gene regulatory mechanisms. Here, we developed in situ SHERRY after ATAC-seq (ISSAAC-seq), a highly sensitive and flexible single cell multi-omics method to interrogate chromatin accessibility and gene expression from the same single cell. We demonstrated that ISSAAC-seq is sensitive and provides high quality data with orders of magnitude more features than existing methods. Using the joint profiles from thousands of nuclei from the mouse cerebral cortex, we uncovered major and rare cell types together with their cell-type specific regulatory elements and expression profiles. Finally, we revealed distinct dynamics and relationships of transcription and chromatin accessibility during an oligodendrocyte maturation trajectory.
2022-06-15 | E-MTAB-11264 | biostudies-arrayexpress
Project description:Affymetrix Mouse Genome 430 2.0 Array was used to perform single-cell transcriptome analysis to unravel the molecular mechanisms underlying the dedifferentiation and cell cycle reentry of mouse adult cardiomyocytes (ACMs). A total of six samples were used for single-cell transcriptome analysis using Affymetrix MG 430 2.0 Array coupled with a microfluidic chip for single cell isolation and NuGen Ovation Single-Cell Amplification technologies. Three biological replicates of adult cardiomyocyte single cells were used as controls and three biological replicates of myocyte-derived progenitor single cells (mCPCs) were used in the experimental group. The whole genome methylome microarray data using NimbleGen Mouse DNA Methylation 3x720K CpG Island Plus RefSeq Promoter Array and genomic DNA derived from population cells for both control adult cardiomyocytes and mCPCs can be found in E-MTAB-3982. The whole genome methylome data using NimbleGen Mouse 2.1M array and genomic DNA derived from population cells for both control adult cardiomyocytes and mCPC can be found in E-MTAB-3984.
2016-03-22 | E-MTAB-3981 | biostudies-arrayexpress
Project description:DNA barcodes can be used to identify single cells in a sequencing data space while optical codes can be used to track single live cells in an image data space. We have developed dual image and DNA (ID)-coding, which identifies individual single cells in both live image and sequencing data spaces. Samples provided here are relevant to proof-of-concept studies of ID-coding presented in the associated publication. DNA barcoded micro-particles were encapsulated in hydrogel droplets with or without single cells. The hydrogel droplets were then subjected to “single-droplet sequencing” where whole polyA-bearing nucleic acid components within a hydrogel droplet (i.e. mRNA from cells and synthetic DNA on beads) were concatenated by the same cell barcodes.
2023-12-11 | E-MTAB-12988 | biostudies-arrayexpress
Project description:In vitro neuronal models are essential for studying neurological physiology, disease mechanisms and potential treatments. Most in vitro models lack controlled vasculature, despite its necessity in brain physiology and disease. Organ-on-chip models offer microfluidic culture systems with dedicated micro-compartments for neurons and vascular cells. Such multi-cell type organs-on-chips can emulate neurovascular unit (NVU) physiology, however there is a lack of systematic data on how individual cell types are affected by culturing on microfluidic systems versus conventional culture plates. This information can provide perspective on initial findings of studies using organs-on-chip models, and further optimizes these models in terms of cellular maturity and neurovascular physiology. Here, we analysed the transcriptomic profiles of co-cultures of human induced pluripotent stem cell (hiPSC)-derived neurons and rat astrocytes, as well as one-day monocultures of human endothelial cells, cultured on microfluidic chips. For each cell type, large gene expression changes were observed when cultured on microfluidic chips compared to conventional culture plates. Endothelial cells showed decreased cell division, neurons and astrocytes exhibited increased cell adhesion, and neurons showed increased maturity when cultured on a microfluidic chip. Our results demonstrate that culturing NVU cell types on microfluidic chips changes their gene expression profiles, presumably due to distinct surface-to-volume ratios and substrate materials. These findings inform further NVU organ-on-chip model optimization and support their future application in disease studies and drug testing.
2021-01-26 | GSE154799 | GEO
Project description:Microfluidic single-cell whole-transcriptome sequencing
| PRJNA208057 | ENA
Project description:Reactive astrocytes are detrimental or protective in ischemic stroke. However, the mechanisms of these effects are not entirely clear. We investigated the heterogeneity of mice astrocytes 12 h after cerebral ischemia-reperfusion via Single-cell RNA sequencing. We acquired astrocyte subclusters’ transcriptional characteristics involving diversified functions. We identified 9 genes as potential therapeutic targets and 6 genes were specific to astrocyte subcluster 2. Additionally, we explored the effects of melatonin and stattic on the transformation of astrocytes to the A2 phenotype. TTC stain, grip strength test and immunofluorescence were used. We revealed melatonin promoted the transformation of astrocytes to the A2 phenotype, the effect was related to STAT3 and inhibited by Stattic. Our study may lay a foundation for untangling the difference between astrocyte subclusters 12 h after stroke and elucidating the mechanisms of A2 astrocyte transformation 3 d after stroke.
2024-09-08 | GSE247474 | GEO
Project description:Spatial omics emerged as a new frontier of biological and biomedical research. Here, we present spatial-CUT&Tag for spatially resolved genome-wide profiling of histone modifications by combining in situ CUT&Tag chemistry, microfluidic deterministic barcoding, and next-generation sequencing. Spatially resolved chromatin states in mouse embryos revealed tissue-type-specific epigenetic regulations in concordance with ENCODE references and provide spatial information at tissue scale. Spatial-CUT&Tag revealed epigenetic control of the cortical layer development and spatial patterning of cell types determined by histone modification in mouse brain. Single-cell epigenomes can be derived in situ by identifying 20-micrometer pixels containing only one nucleus using immunofluorescence imaging. Spatial chromatin modification profiling in tissue may offer new opportunities to study epigenetic regulation, cell function, and fate decision in normal physiology and pathogenesis.
2022-02-10 | GSE165217 | GEO
Project description:Saccharomyces cerevisiae wildtype (YPH) and ung1-deleted strains were cultivated in mutation accumulation experiments over several bottlenecks (0-50-100-150). Two different cutlure systems were used either (i) using random colony selection and plating on petri dish (classical); or (ii) a microfluidic-based system (microfluidic)
2021-08-01 | E-MTAB-10259 | biostudies-arrayexpress