slide seqv2 datasets5 Search Results


slide seqv2 datasets5  (Broad Clinical Labs)
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Broad Clinical Labs slide seqv2 datasets5
Spatial domain identification and biological validation in the mouse olfactory bulb dataset <t>by</t> <t>Slide-seqV2</t> : (A) Laminar organization of mouse olfactory bulb annotated by the Allen Reference Atlas; (B) comparison of spatial domains identified by SpatialDG and Spatial-MGCN, SEDR; (C) spatial expression heatmaps of eight representative layer-specific marker genes (Gabra1, Slc6a11, Mbp, Atp2b4, Pcp4, Nrgn, Cck, Kctd12), with color intensity indicating expression levels; (D) violin plot of domain-marker gene expressions in derived clusters by SpatialDG.
Slide Seqv2 Datasets5, supplied by Broad Clinical Labs, used in various techniques. Bioz Stars score: 96/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Spatial domain identification and biological validation in the mouse olfactory bulb dataset by Slide-seqV2 : (A) Laminar organization of mouse olfactory bulb annotated by the Allen Reference Atlas; (B) comparison of spatial domains identified by SpatialDG and Spatial-MGCN, SEDR; (C) spatial expression heatmaps of eight representative layer-specific marker genes (Gabra1, Slc6a11, Mbp, Atp2b4, Pcp4, Nrgn, Cck, Kctd12), with color intensity indicating expression levels; (D) violin plot of domain-marker gene expressions in derived clusters by SpatialDG.

Journal: Briefings in Bioinformatics

Article Title: SpatialDG: a novel spatial domain identification method for spatially resolved transcriptomics data based on dual-graph neural network

doi: 10.1093/bib/bbag145

Figure Lengend Snippet: Spatial domain identification and biological validation in the mouse olfactory bulb dataset by Slide-seqV2 : (A) Laminar organization of mouse olfactory bulb annotated by the Allen Reference Atlas; (B) comparison of spatial domains identified by SpatialDG and Spatial-MGCN, SEDR; (C) spatial expression heatmaps of eight representative layer-specific marker genes (Gabra1, Slc6a11, Mbp, Atp2b4, Pcp4, Nrgn, Cck, Kctd12), with color intensity indicating expression levels; (D) violin plot of domain-marker gene expressions in derived clusters by SpatialDG.

Article Snippet: All the datasets used in this paper are open access and available as (1) The LIBD human dorsolateral prefrontal cortex (DLPFC) dataset http://spatial.libd.org/spatialLIBD ; (2) 10x Visium spatial transcriptomics dataset of human breast cancer https://support.10xgenomics.com/spatial-gene-expression/datasets/1.1.0/V1_Breast_Cancer_Block_A_Section_1 ; (3) Mouse embryo Stereo-seq data https://db.cngb.org/stomics/mosta/ ; (4) Slide-seqV2 datasets5 are available at the Broad Institute Single Cell Portal at https://singlecell.broadinstitute.org/single_cell/study/SCP815/highly-sensitive-spatial-transcriptomics-at-near-cellular-resolution-with-slide-seqv2#study-summary .

Techniques: Biomarker Discovery, Olfactory, Comparison, Expressing, Marker, Derivative Assay