mouse olfactory bulb dataset  (Complete Genomics Inc)

Journal: Briefings in Bioinformatics

Article Title: SpaGIC: graph-informed clustering in spatial transcriptomics via self-supervised contrastive learning

doi: 10.1093/bib/bbae578

Figure Lengend Snippet: Spatial domains identification on the Stereo-seq MOB dataset. ( A ) The laminar structure of the Stereo-seq MOB annotated in DAPI-stained images. ( B ) Clustering results from Scanpy, SpaGCN, DeepST, STAGATE, GraphST, and SpaGIC. ( C ) Visualization of spatial domains detected by SpaGIC and related marker gene expression.

Article Snippet: Specifically, (i) the LIBD human dorsolateral prefrontal cortex (DLPFC) dataset: http://spatial.libd.org/spatialLIBD/ ; (ii) the 10x Visium human breast cancer dataset: https://www.10xgenomics.com/datasets/human-breast-cancer-block-a-section-1-1-standard-1-1-0 ; (iii) the anterior section of the 10x Visium mouse brain: https://www.10xgenomics.com/resources/datasets/mouse-brain-serial-section-1-sagittal-anterior-1-standard-1-1-0 ; (iv) the Stereo-seq mouse olfactory bulb dataset: https://github.com/STOmics/SAW/tree/main/Test_Data ; (v) the Slide-seqV2 mouse olfactory bulb dataset: https://singlecell.broadinstitute.org/single_cell/study/SCP815/highly-sensitive-spatial-transcriptomics-at-near-cellular-resolution-with-slide-seqv2#study-summary ; (vi) the STARmap mouse visual cortex dataset: https://drive.google.com/drive/folders/1I1nxheWlc2RXSdiv24dex3YRaEh780my?usp=sharing ; (vii) the osmFISH mouse somatosensory cortex dataset: https://linnarssonlab.org/osmFISH/ .

Techniques: Staining, Marker, Gene Expression

Journal: Nucleic Acids Research

Article Title: STAMarker: determining spatial domain-specific variable genes with saliency maps in deep learning

doi: 10.1093/nar/gkad801

Figure Lengend Snippet: STAMarker reveals the domain-specific SVGs on the mouse olfactory bulb dataset. ( A ) Spatial domains identified by STAMarker. The laminar organization of the mouse olfactory bulb is clearly shown. The identified spatial domains were annotated by the Allen Reference Atlas. ( B ) Histogram of the number of spatial domains to which the SVGs identified by STAMarker belong. ( C ) UpSet plot of the numbers of SVGs identified by STAMarker and six compared methods. STAMarker identified 311 SVGs. ( D ) Heatmap showing the eight modules that were clustered by the 67 domain-specific SVGs. ( E ) Visualization of the domain-specific gene modules by the first principal component of the saliency maps. ( F ) Visualization of the representative spatial domain-specific SVGs.

Article Snippet: The human lymph node and mouse olfactory bulb datasets are available at 10x genomics website 10xgenomics.com/resources/datasets hippocampus dataset of the J20 mouse model generated by Slide-seq V2 is accessible at https://singlecell.broadinstitute.org/single_cell/study/SCP1663/cell-type-specific-inference-of-differential-expression-in-spatial-transcriptomics .

Techniques: