Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Protecting RNA Integrity for Spatial Transcriptomics While Improving Immunofluorescent Staining Quality

ABSTRACT: In comparison to bulk sequencing or single cell sequencing, spatial transcriptomics preserves the spatial information in tissue slices and can even be mapped to immunofluorescent stainings. This enables to unravel complex interactions of neighboring cells or to link cell morphology to transcriptome data. The 10x genomics visium spatial assay offers to combine spatial transcriptomics with immunofluorescent staining of cryo-sectioned tissue slices. We applied this technique to 10 µm fresh frozen mouse brain slices and developed a protocol that still protects RNA integrity while improving buffers for immunofluorescent staining. We investigated the influence of various parameters on RNA integrity and on antibody binding of blocking, staining as well as wash buffers. Finally, we propose a protocol that does not alter RNA integrity in comparison the 10x genomics demonstrated protocol but allows the usage of several antibodies that have not been compatible with the protocol before. In addition, we discuss the influence of the tested parameters which offers further development of application specific staining protocols.

ORGANISM(S): Mus musculus

PROVIDER: GSE228891 | GEO | 2023/06/07

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Protecting RNA Integrity for Spatial Transcriptomics While Improving Immunofluorescent Staining Quality

Project description:Protecting RNA Integrity for Spatial Transcriptomics While Improving Immunofluorescent Staining Quality

| PRJNA951864 | ENA

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).

2024-07-23 | E-MTAB-12105 | biostudies-arrayexpress

Spatial transcriptomics: The effect of consecutive slices data integration on accurate cell type annotation and clustering

Project description:In 10X Genomics Visium Spatial Gene Expression (ST), the resolution for distinguishing neighboring cells can be improved using data integration with single-cell/single-nuclei transcriptomics profiles. Besides, depending on the cell type and tissue, nuclei size may vary significantly to an extent that it may exceed the thickness of tissue slices. This may jeopardize capturing full transcriptomics profile of single slice due to the improper/incomplete incision of nuclei during cryosectioning process and this may cause drawbacks in downstream analysis. To monitor the probable consequences, we monitored the effect of consecutive slices data integration (CSDI) on improvement of cell type clustering and annotation through transferring cell labels from a single-nuclei transcriptomics dataset to ST. To do so, two consecutive slices from the orbitofrontal neocortex and temporal neocortex of two post mortem brain samples were obtained and their spatial transcriptomics profiles were retrieved using 10x Genomics Visium Spatial Gene Expression protocol. Using CSDI, not only the number of identified clusters were increased and the inconsistency between the pattern of clusters in consecutive slices was resolved, but the layered-structure of gray matter was unveiled. Besides, only after CSDI the transferred annotations from single-nuclei transcriptomics to ST could match the microscopic results. CSDI can improve the ST clustering and cell type annotation by providing the full signals coming from all cell types of single slice of tissue. The codes in R programming language are publicly available at https://github.com/ElyasMo/ST_snRNA-seq

2023-05-12 | GSE184510 | GEO

Spatial transcriptomics on human dorsal root ganglion (DRG)

Project description:Visium Spatial Gene Expression by the 10X genomics protocol was performed on 2 sections of human DRG tissue to elucidate the spatial transcriptomic organization.

2023-09-14 | GSE215994 | GEO

Single cell- Cluster-RNA seq and Spatial Transcriptomics from the trunk of mouse embryos of different genotypes (wild type, Pax2-GFP, Pax2-GFP; Gata3 knockout) and developmental stages (E8.75, E9.5, E11.5) [Spatial Transcriptomics]

Project description:To study cell heterogeneity and state transitions in the developing urinary tract we performed spatial transcriptomics from the trunk of E9.5 Pax2GFP mouse embryos using the 10X Genomics Visium Spatial Gene Expression protocol

2021-02-16 | GSE160137 | GEO

NanoString nCounter NF1-mutant melanoma gene expression

Project description:Purpose: Digital spatial profiling was used to elucidate the interplay between the tumor cells and the surrounding microenvironment FFPE tissues. Methods: Two tissue microarrays (TMA) were generated from each FFPE block using the ISNET Galileo CK4500 computer-driven tissue microarray. Images of H&E-stained cores were demarcated by a pathologist and were utilized alongside NanoString immunofluorescent staining for morphology markers S100, CD45, CD3, and DAPI to draw region of interest.

2022-04-16 | GSE200904 | GEO

Lineage recording in human cerebral organoids (Visium)

Project description:Induced pluripotent stem cell (iPSC) derived organoid systems provide models to study human organ development. Single-cell transcriptome sequencing enables highly-resolved descriptions of cell state heterogeneity within these systems and computational methods can reconstruct developmental trajectories. However, new approaches are needed to directly measure lineage relationships in these systems. Here we establish an inducible dual channel lineage recorder, iTracer, that couples reporter barcodes, inducible CRISPR/Cas9 scarring, and single-cell transcriptomics to analyze state and lineage relationships in iPSC-derived systems. This data set include the spatial iTracer data of three slices of one cerebral organoid measured by 10x Visium.

2021-11-03 | E-MTAB-10972 | biostudies-arrayexpress

Spatial transcriptomics of post-mortem lung tissue from COVID-19 donors

Project description:Visualization of gene expression in lung tissue was performed using Visium spatial gene expression kits (10x Genomics) following the manufacturer`s protocol. The four capture areas in a 10x Genomics Visium Gene Expression slide consist of 5000 spots with DNA oligos for mRNA capture that have a unique spatial barcode and a unique Molecular Identifier (UMI). Each spot has 55 µm diameter and can therefore capture mRNA from 1 to 10 cells. We report the spatially resolved transcriptome of 3 control lung samples from non-COVID-19-related pneumonia donors and 9 COVID-19 lung samples analyzed with the 10x Visium platform.

2022-12-21 | GSE190732 | GEO

Single cell RNA-seq of ten-thousand epithelium cells from the mammary glands of mice in puberty, estrus and diestrus phases

Project description:Epithelial cells were isolated by FACS from the mammary glands of pubescent (5 week old), estrus adult (10 week old) and diestrus adult (10 week old) female mice. Freshly sorted cells were submitted to a 10X Genomics Chromium System for single cell capture. cDNA synthesis and library preparation was done according to the protocol supplied by the manufacturer. Sequencing was carried out on an Illumina NextSeq500 sequencer using parameters recommended by 10X Genomics.

2017-11-20 | GSE103272 | GEO

Spatial transcriptomic analyses of distal colon cross-sections from mice fed high fiber and control diet

Project description:To perform a global analysis of high fiber diet-induced changes in gene expression in various compartments of the colonic microenvironment, we employed a spatial transcriptomic analysis using the 10X Genomics® platform. This technique allowed for visualization of gene expression in histological cross-sections of the distal colon with spatial information and therefore enabled detection of differentially expressed genes simultaneously in diverse cell types, together with information about their anatomical location in the tissue. Distal colon samples were processed using a Visium Spatial Gene Expression Slide & Reagent Kit (PN-1000184, 10X Genomics) as per the manufacturer’s instructions. Unbiased clustering divided the colon into four distinct zones: epithelium, lamina propria & submucosa, muscularis, and neuronal plexus, as visualized by hematoxylin and eosin (H&E) staining.

2022-08-17 | GSE183696 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data