Molecular and spatial analysis of ganglion cells on retinal flatmounts: diversity, topography, and perivascularity

Summary:

Processed datasets from applying MERFISH spatial transcriptomics to wholemount retina. Raw imaging data will be hosted at a separate link.

Uploaded Data:

Anndata objects

1.merged_control.h5adRRaw concatenated cell by gene matrices across many retinae

2. merged_control_cluster_final_mapped.h5adFinal preprocessed cell by gene matrix.

3. RGC_control_mapped.h5adRGC only preprocessed matrix (a subset of the dataset above)

4. Melanopsin_runs.h5ad

Processed RGC matrix of MERFISH runs with Melanopsin antibody staining (Cellbound3 column in adata.obs)

Additional supplementary data

5. column_info.txtDescription of metadata in columns of .h5ad files. The most important columns are: 'final_x', 'final_y' (spatial coordinates of cells), 'run' (Retina ID), 'region' (Tissue section ID), 'class' (Cell class), 'final_assignment': (Cell type assignment).

6. Spline_coordinates.jsonSplines for the outline of each retina used in certain figures (e.g. Figure S6)

7. Exclusion_areas.zipFor Figure S7 (mosaic analysis). Contains json files, one for each ROI, containing polygons for ROI bounds as well as outlining major holes.