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

Journal: Biology

Article Title: The Advancement and Application of the Single-Cell Transcriptome in Biological and Medical Research

doi: 10.3390/biology13060451

Figure Lengend Snippet: Applications of single-cell transcriptome sequencing in different fields. ( a ) Large-scale cell mapping construction, the first whole-body organellar transcriptome mapping in a non-human primate, the rhesus macaque . ( b ) Oncology research: pan-cancer analyses on bone marrow cells from 210 patients with 15 different human cancer types using single-cell transcriptome sequencing . ( c ) Neuroscience research: hippocampus of humans, rhesus monkeys, and pigs . ( d ) Developmental biology: human prefrontal cortex gene expression from gestation to adulthood , embryo and Arabidopsis leaves . ( e ) Cell subpopulation refinement and rare cell type identification: liver and kidney . ( f ) Stem cells research: resurrection stem cells in the mouse intestine, which can be activated through injury . ( g ) Applications in microbiology: protocols for bacterial single-cell transcriptomics . ( h ). Single-cell transcriptome reveals drug resistance in cancer cells. ( i ) Integration and utilization of single-cell datasets: “anchor” different datasets together, which not only integrates single-cell sequencing data with different scRNA-seq technologies, but also integrates single-cell sequencing data with different modalities .

Article Snippet: Although Spatial Transcriptomics (ST-seq) can obtain both spatial location information and the gene expression data of cells, it currently falls short of single-cell precision.

Techniques: Sequencing, Gene Expression, Single-cell Transcriptomics

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: To better characterize the expression pattern of bacteriocyte lineages, we employed two groups of deep-sea mussels in the present study and conducted both single-cell transcriptome (scRNA-seq, Chromium platform of 10x Genomics) and spatial transcriptomics (ST-seq, Visium platform of 10x Genomics) analysis ( ).

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: To better characterize the expression pattern of bacteriocyte lineages, we employed two groups of deep-sea mussels in the present study and conducted both single-cell transcriptome (scRNA-seq, Chromium platform of 10x Genomics) and spatial transcriptomics (ST-seq, Visium platform of 10x Genomics) analysis ( ).

Techniques: Immunofluorescence

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

Journal: NPJ Precision Oncology

Article Title: High risk clear cell renal cell carcinoma microenvironments contain protumour immunophenotypes lacking specific immune checkpoints

doi: 10.1038/s41698-023-00441-5

Figure Lengend Snippet: The patient characteristics ( a ) of the six ccRCC patients ( n = 3 LG and n = 3 HG) include: patient LG_2 with a vena cava thrombus (VCT) for which we collected primary tumour microenvironment (TME) and thrombi separately but processed in the one capture array for ST-seq; patient HG_1 that we collected and processed tissues from para-TME (pTME) and TME; and patient HG_3 that we collected tissues from pTME and TME. For this experimental workflow ( b ), ten tissue regions were sampled from pTME, TME and VCT that excluded fibrotic and necrotic regions. ST-seq was completed using 10x Genomics Visium Gene Expression microarrayed glass slides with unique spatially barcoded ST-spots that captured the mRNA released from the overlaying thin ccRCC tissue sections. Annotation of immune ST-spots was completed with data integration of six published single-cell RNA-sequencing (scRNA-seq) datasets. Further immune cell sub-typing was completed with a scRNA and T-cell receptor (TCR) sequencing dataset. Integrated analysis was completed on CD8 + T cells, TAM and monocytes.

Article Snippet: To profile the transcriptome within the ccRCC TME, we performed ST-seq using Visium Spatial Gene Expression (CG000239 Rev D, 2020 October, 10x Genomics, USA) on ten fresh frozen tissue sections collected in the operating theatre from six patients with ccRCC ( n = 2 pTME, n = 4 LG and n = 4 HG) presenting at a tertiary referral hospital from June 2021 to January 2022 (Fig. ).

Techniques: Gene Expression, RNA Sequencing, Sequencing