Similar Datasets
Project description:This SuperSeries is composed of the SubSeries listed below.
2023-06-21 | GSE202638 | GEO
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
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
Project description:Spatial Transcriptomics correlated Electron Microscopy
| PRJNA836860 | ENA
Project description:Cells are 3D objects. Therefore, volume EM (vEM) is often crucial for correct interpretation of ultrastructural data. Today, scanning EM (SEM) methods such as focused ion beam (FIB)-SEM are frequently used for vEM analyses. While they allow automated data acquisition, precise targeting of volumes of interest within a large sample remains challenging. Here, we provide a workflow to target FIB-SEM acquisition of fluorescently labeled cells or subcellular structures with micrometer precision. The strategy relies on fluorescence preservation during sample preparation and targeted trimming guided by confocal maps of the fluorescence signal in the resin block. Laser branding is used to create landmarks on the block surface to position the FIB-SEM acquisition. Using this method, we acquired volumes of specific single cells within large tissues such as 3D cultures of mouse mammary gland organoids, tracheal terminal cells in Drosophila melanogaster larvae, and ovarian follicular cells in adult Drosophila, discovering ultrastructural details that could not be appreciated before.
| S-EPMC8225610 | biostudies-literature
Project description:Spatial Transcriptomics correlated Electron Microscopy [MERFISH]
| PRJNA836863 | ENA
Project description:Volume electron microscopy (EM) is a time-consuming process - often requiring weeks or months of continuous acquisition for large samples. In order to compare the ultrastructure of a number of individuals or conditions, acquisition times must therefore be reduced. For resin-embedded samples, one solution is to selectively target smaller regions of interest by trimming with an ultramicrotome. This is a difficult and labour-intensive process, requiring manual positioning of the diamond knife and sample, and much time and training to master. Here, we have developed a semi-automated workflow for targeting with a modified ultramicrotome. We adapted two recent commercial systems to add motors for each rotational axis (and also each translational axis for one system), allowing precise and automated movement. We also developed a user-friendly software to convert X-ray images of resin-embedded samples into angles and cutting depths for the ultramicrotome. This is provided as an open-source Fiji plugin called Crosshair. This workflow is demonstrated by targeting regions of interest in a series of Platynereis dumerilii samples.
| S-EPMC9665851 | biostudies-literature
Project description:Spatial Transcriptomics correlated Electron Microscopy [scRNA-Seq]
| PRJNA836864 | ENA
Project description: Not available
| EMPIAR-11055 | biostudies-other
Project description:The development of plasma-based accelerators has enabled the generation of very high brightness electron bunches of femtosecond duration, micrometer size and ultralow emittance, crucial for emerging applications including ultrafast detection in material science, laboratory-scale free-electron lasers and compact colliders for high-energy physics. The precise characterization of the initial bunch parameters is critical to the ability to manipulate the beam properties for downstream applications. Proper diagnostic of such ultra-short and high charge density laser-plasma accelerated bunches, however, remains very challenging. Here we address this challenge with a novel technique we name as femtosecond ultrarelativistic electron microscopy, which utilizes an electron bunch from another laser-plasma accelerator as a probe. In contrast to conventional microscopy of using very low-energy electrons, the femtosecond duration and high electron energy of such a probe beam enable it to capture the ultra-intense space-charge fields of the investigated bunch and to reconstruct the charge distribution with very high spatiotemporal resolution, all in a single shot. In the experiment presented here we have used this technique to study the shape of a laser-plasma accelerated electron beam, its asymmetry due to the drive laser polarization, and its beam evolution as it exits the plasma. We anticipate that this method will significantly advance the understanding of complex beam-plasma dynamics and will also provide a powerful new tool for real-time optimization of plasma accelerators.
| S-EPMC10172298 | biostudies-literature