Journal: eLife

Article Title: Heterochronic transcription factor expression drives cone-dominant retina development in 13-lined ground squirrels

doi: 10.7554/eLife.108485

Figure Lengend Snippet: ( A ) Schematic illustrating annotation of cis -regulatory elements in RPCs and photoreceptor precursors by integration of scATAC-Seq and CUT&RUN 13LGS and mouse datasets. ( B ) Heatmaps show annotated accessible regulatory elements in both 13LGS and mouse. Promoters, activated enhancers (AEs), and poised enhancers (PEs), which are associated with histone markers associated with genes in clusters C2 and C3, which are selectively active in 13LGS RPCs and/or photoreceptor precursors. Shading indicates CUT&TAG signal for the corresponding histone modification within 2 kb of the scATAC-Seq peak center. Bar plots displaying the number of each category of regulatory element in each species that are conserved or species-specific. ( C ) Dot plots showing the enrichment of binding sites for Otx2 and Neurod1, TFs which are broadly expressed in both neurogenic RPC and photoreceptor precursors, which are enriched in both conserved cis -regulatory elements in both species. ( D ) Bar plots showing the number of conserved and species-specific enhancers per transcription start site (TSS) in four cone-promoting genes between 13LGS and mouse. ( E ) The gene regulatory networks (GRNs) regulating Thrb expression in 13LGS and mouse late N. RPCs. ( F ) An example of a Thrb-related regulon and its corresponding scATAC-Seq and CUT&RUN tracks. The arrow indicates the consistent regulatory relationships between GRN prediction and experimental validations. ( G ) The epigenetic model of cone specification in 13LGS and mouse.

Article Snippet: Antibody , H3K4me3 Antibody, SNAP-Certified for CUT&RUN , EpiCypher , 13-0041 , 0.41 μg/reaction.

Techniques: Modification, Binding Assay, Expressing

Journal: eLife

Article Title: Heterochronic transcription factor expression drives cone-dominant retina development in 13-lined ground squirrels

doi: 10.7554/eLife.108485

Figure Lengend Snippet: ( A ) Gene regulatory networks controlling Zic3 expression in 13LGS late-stage neurogenic RPCs, photoreceptor precursors, and cones. ( B ) Example of Zic3-related regulons and their corresponding scATAC-Seq and CUT&RUN tracks in 13LGS. ( C ) Example of Zic3-related regulons and their corresponding scATAC-Seq and CUT&RUN tracks in mouse.

Article Snippet: Antibody , H3K4me3 Antibody, SNAP-Certified for CUT&RUN , EpiCypher , 13-0041 , 0.41 μg/reaction.

Techniques: Expressing

Journal: bioRxiv

Article Title: YAP disrupts bile acid homeostasis to drive cancer-associated cachexia

doi: 10.64898/2026.02.01.702698

Figure Lengend Snippet: a , Schematic of the spatial transcriptomics (SRT) workflow. Cryosections were obtained from the indicated anatomical region (highlighted in schematic). Adjacent sister sections were stained with H&E, and sections for SRT were processed with BGI Stereo-seq technology. b , Spatial feature plot showing spot-level transcriptomic clustering of WT and PY-TB zebrafish samples. Clusters were identified by Seurat using principal component analysis and graph-based clustering of transcriptomic neighbourhoods. c , Integrated UMAP of all spatial transcriptomic spots coloured by Seurat-defined cluster identity. Cluster annotation was guided by regionally enriched marker genes and tissue interpretation using Zebrahub. d , UMAP and spatial feature plots highlighting hepatocyte-enriched spots defined by expression of hepatocyte marker, fabp10a , above the 75th percentile. Cells are grouped by sample: WT hepatocytes (blue) and PY-TB hepatocytes (red). e , Volcano plot of differentially expressed genes (DEGs) between PY-TB hepatocytes and WT hepatocytes, both defined by fabp10a expression in the spatial data. f , Spatial projection of cholangiocyte marker, anxa4, expression, visualised over spatial coordinates of the tissue section. g-i , Gene set enrichment analysis (GSEA) plots of selected pathways enriched in PY-TB hepatocytes versus WT, derived from DEGs identified in the SRT dataset. j , H&E and immunofluorescence staining of liver sections of WT and PY-TB fish at 21 dpf. Nuclei are marked with DAPI (cyan), hepatocytes with GFP (green), and cholangiocytes with ANXA4 (magenta). White arrow represents GFP+/ANXA4+ bi-lineage cells. Scale bar, 100 μm.

Article Snippet: Frozen tissue blocks were stored at −80 °C and cryosectioned at 10 μm onto STOmics Stereo-seq chips (V1.1; BGI Research).

Techniques: Spatial Transcriptomics, Staining, Marker, Expressing, Derivative Assay, Immunofluorescence