spatial transcriptome rna sequencing (strna-seq) data for breast cancer samples, specific to the 10x visium platform  (10X Genomics)

Journal: bioRxiv

Article Title: Cooperation between bacteriocytes and endosymbionts drives function and development of symbiotic cells in mussel holobionts

doi: 10.1101/2023.08.18.553804

Figure Lengend Snippet: (A) Experimental workflow for, and analysis of, single-cell transcriptome (scRNA-seq) and spatial transcriptome (ST-seq) of gill tissue in fully symbiotic (InS group) and partially decolonized (DeC) deep-sea mussels. A marked decrease of the endosymbiont is observed after in situ translocation assay (n=14 for the InS group, n=5 for the DeC group). (B) t-SNE projection of spatial transcriptome clustered by gene expression in the InS group, with color assigned by cell type (left). Projection of cell clusters onto spatial transcriptome barcoded spots (right) in the InS group. Two successive sections were used in the same capture region of spatial transcriptome as technique replicates. (C) t-SNE projection of single-cell transcriptome clustered by gene expression in the InS group, with color assigned by cell type (left). Spatial transcriptome barcoded spots labeled using scRNA-seq cell type with maximum prediction score (right). (D) Fluorescent in situ hybridization (FISH) of endosymbionts with successive gill sections for ST-seq (InS group) and ISH of bacteriocytes marker genes.

Article Snippet: Only one mussel from the InS group was used for single cell transcriptome sequencing (scRNA-seq, Chromium platform of 10x Genomics, Pleasanton CA, USA) and spatial transcriptome sequencing (ST-seq, Visium platform of 10x Genomics), and all 14 mussels collected by isothermal isobaric sampler or after RNA stabilizing treatment were subjected to meta-transcriptome sequencing.

Techniques: In Situ, Translocation Assay, Gene Expression, Labeling, In Situ Hybridization, Marker

Journal: bioRxiv

Article Title: Cooperation between bacteriocytes and endosymbionts drives function and development of symbiotic cells in mussel holobionts

doi: 10.1101/2023.08.18.553804

Figure Lengend Snippet: (A) ScRNA/ST-seq and meta-transcriptome data show an intimate interaction of sterol metabolism between the host and symbionts. In support of this, immunofluorescence (IF) assay (using gills of the InS group) of the 24-hydroxycholesterol 7 alpha-hydroxylase (CYP39A1) protein shows that CYP39A1 proteins are widely distributed across bacteriocytes. In addition, a more intensive signal of CYP39A1 protein could also be observed at the apical region that enriched with endosymbionts (indicated by lipid A signals). (B) ScRNA/ST-seq and meta-transcriptome data show intimate interaction of glucose/glycogen metabolism between the host and symbionts. In support of this, IF assay of the sugar phosphate exchanger (SLC37A2) protein shows the co-location of SLC37A2 proteins with endosymbionts inside bacteriocytes. (C) ScRNA/ST-seq and meta-transcriptome data show intimate interactions of ammonia metabolism between the host and symbionts. In support of this, IF assay of the ammonium transporter Rh (RHBG-A) protein shows co-location of RHBG-A proteins with endosymbionts inside bacteriocytes.

Article Snippet: Only one mussel from the InS group was used for single cell transcriptome sequencing (scRNA-seq, Chromium platform of 10x Genomics, Pleasanton CA, USA) and spatial transcriptome sequencing (ST-seq, Visium platform of 10x Genomics), and all 14 mussels collected by isothermal isobaric sampler or after RNA stabilizing treatment were subjected to meta-transcriptome sequencing.

Techniques: Immunofluorescence