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Seq-Scope: Submicrometer-resolution spatial barcoding technology that enables microscopic examination of tissue transcriptome at single cell and subcellular levels

ABSTRACT: Seq-Scope: Submicrometer-resolution spatial barcoding technology that enables microscopic examination of tissue transcriptome at single cell and subcellular levels

PROVIDER: PRJNA717741 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR14082751.fastq.gz	Fastqsanger.gz
	SRR14082752.fastq.gz	Fastqsanger.gz
	SRR14082753_1.fastq.gz	Fastqsanger.gz
	SRR14082753_2.fastq.gz	Fastqsanger.gz
	SRR14082754_1.fastq.gz	Fastqsanger.gz

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Seq-Scope: Submicrometer-resolution spatial barcoding technology that enables microscopic examination of tissue transcriptome at single cell and subcellular levels

Project description:Purpose: we propose Sequence-Scope (Seq-Scope), which can generate ultra-high definition images of sequence-based molecular signatures resolved at a submicrometer scale. Experimental Methods: Seq-Scope experiment is divided into two consecutive sequencing steps: 1st-Seq and 2nd-Seq. 1st-Seq of Seq-Scope starts with the solid-phase amplification of a single-stranded synthetic oligonucleotide library using an Illumina sequencing-by-synthesis (SBS) platform. 2nd-Seq of Seq-scope begins with overlaying the tissue section slice onto the HDMI-array. Computational Methods: Tissue boundaries are detected by using a custom python code to draw a smoothed density plot to visualize the density of HiSeq reads in a given XY space of each tile. Digital gene expression (DGE) matrices are generate using STAR/STARsolo 2.7.5c with Gene,GeneFull, Velocyto, and polyAtrimming options. Data binning is performed by dividing the imaging space into 100 μm2 square grid with 10 μm simple side or 25 μm2 square grid with 5 μm side and collapsing all HDMI-UMI information into one barcode. Binned DGE matrix was analyzed in the Seurat v4 package for clustering analysis.

2021-04-19 | GSE169706 | GEO

Microscopic examination of spatial transcriptome using Seq-Scope.

Project description:Spatial barcoding technologies have the potential to reveal histological details of transcriptomic profiles; however, they are currently limited by their low resolution. Here, we report Seq-Scope, a spatial barcoding technology with a resolution comparable to an optical microscope. Seq-Scope is based on a solid-phase amplification of randomly barcoded single-molecule oligonucleotides using an Illumina sequencing platform. The resulting clusters annotated with spatial coordinates are processed to expose RNA-capture moiety. These RNA-capturing barcoded clusters define the pixels of Seq-Scope that are ∼0.5-0.8 μm apart from each other. From tissue sections, Seq-Scope visualizes spatial transcriptome heterogeneity at multiple histological scales, including tissue zonation according to the portal-central (liver), crypt-surface (colon) and inflammation-fibrosis (injured liver) axes, cellular components including single-cell types and subtypes, and subcellular architectures of nucleus and cytoplasm. Seq-Scope is quick, straightforward, precise, and easy-to-implement and makes spatial single-cell analysis accessible to a wide group of biomedical researchers.

| S-EPMC8238917 | biostudies-literature

MESO-SCOPE, SCOPE cruise July 2017

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Seq-Scope analysis of human acne

Project description:Skin samples were analyzed through Seq-Scope.

2022-07-22 | GSE186601 | GEO

SCOPE FALKOR Eukaryotic Metatranscriptomes

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Seq-Scope profiling of mouse colon sections with biopsy-induced injuries

Project description:We used Sequence-Scope (Seq-Scope), which can generate ultra-high definition images of sequence-based molecular signatures resolved at a submicrometer scale, for profiling spatial transcriptome associated with biopsy-associated colon injury. Raw 1st-Seq FASTQ with intact tile and coordinate information could be retrieved from https://doi.org/10.5281/zenodo.13118097

2024-08-29 | GSE266556 | GEO

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