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Spatial Transcriptomics correlated Electron Microscopy [scRNA-Seq]

ABSTRACT: Spatial Transcriptomics correlated Electron Microscopy [scRNA-Seq]

PROVIDER: PRJNA836864 | ENA |

REPOSITORIES: ENA

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Spatial Transcriptomics correlated Electron Microscopy

Project description:Spatial Transcriptomics correlated Electron Microscopy

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Spatial Transcriptomics correlated Electron Microscopy [MERFISH]

Project description:Spatial Transcriptomics correlated Electron Microscopy [MERFISH]

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Spatial Transcriptomics correlated Electron Microscopy [scRNA-Seq]

Project description:Current spatial transcriptomics methods identify cell types and states in a spatial context but lack morphological information. Electron microscopy, in contrast, provides structural details at nanometer resolution without decoding the diverse cellular states and identity. STEM address this limitation by correlating multiplexed error-robust FISH with electron microscopy from adjacent tissue sections. Using STEM to characterize demyelinated lesions in mice, we were able to bridge spatially resolved transcriptional data with morphological information on cell identities. This approach allowed us to link the morphology of foamy microglia and interferon-response microglia with their transcriptional signatures.

2023-06-21 | GSE202636 | GEO

Spatial Transcriptomics correlated Electron Microscopy [MERFISH]

Project description:Current spatial transcriptomics methods provide molecular and spatial information but no morphological readout. Here, we present STEM - a method that correlates multiplexed error-robust FISH with electron microscopy from neighboring tissue sections of the same sample. STEM links transcriptional and spatial organization of single cells with ultrastructural morphology of the tissue in vivo. Using STEM to characterize demyelinated white-matter lesions allowed us to link morphology of myelin-laden foamy microglia to transcriptional signature. Moreover, we revealed that interferon-response microglia have unique morphology and are enriched near CD8 T-cells.

2023-06-21 | GSE202623 | GEO

Spatial Transcriptomics correlated Electron Microscopy

Project description:This SuperSeries is composed of the SubSeries listed below.

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Primary ciliary dyskinesia without obvious electron microscopy defects

Project description:Primary ciliary dyskinesia without obvious electron microscopy defects

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Primary ciliary dyskinesia without obvious electron microscopy defects

Project description:Primary ciliary dyskinesia without obvious electron microscopy defects

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Spatial transcriptomics of 3-month-old and 18-month-old mouse ovarian and uterine tissues

Project description:We used Visium technology (10X Genomics) to infer cell-to-cell communication in ovarian and uterine tissue based on spatial proximity. Organs from 3-month mice in diestrus and 18-month old mice were collected and frozen in OCT. 10 µm thick tissue slices were placed on Visium Spatial Gene Expression Slides (10X Genomics) and stained with Hematoxylin and Eosin (H&E). Libraries were prepared by manufacturer’s recommendations and sequenced on NovaSeq6000. For samples that were sequenced in two runs, both sequencing runs were merged when running spaceranger (10X Genomics). Original nd2 microscopy images and results of scRNA-seq (linked datasets) and spatial transcriptomics analysis are available at Biostudies (S-BIAD482 and S-BSST852).

2024-01-30 | E-MTAB-12105 | biostudies-arrayexpress

Spatial transcriptomics of fetal skin

Project description:Spatial organization of different cell types within prenatal skin across various anatomical sites is not well understood. To address this, here we have generated spatial transcriptomics data from prenatal facial and abdominal skin obtained from a donor at 10 post conception weeks. This in combination with our prenatal skin scRNA-seq dataset has helped us map the location of various identified cell types.

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Single-cell and spatial transcriptomics reveal somitogenesis in gastruloids

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2019-12-05 | GSE123187 | GEO

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