An ON-type direction selective ganglion cell in primate retina
Data files
Oct 25, 2023 version files 64.66 GB
-
EDF_1.zip
22.32 GB
-
EDF_2.zip
1.17 GB
-
EDF_3.zip
433.09 MB
-
EDF_4.zip
302 B
-
EDF_5.zip
317.71 MB
-
EDF_6.zip
1.13 KB
-
EDF_7.zip
187.11 MB
-
EDF_8.zip
1.48 GB
-
Figure_1.zip
24.14 GB
-
Figure_2.zip
1.02 GB
-
Figure_3.zip
10.02 GB
-
Figure_4.zip
3.57 GB
-
README.md
4.92 KB
Abstract
To maintain a stable and clear image of the world, our eyes reflexively follow the direction in which a visual scene is moving. Such gaze stabilisation mechanisms reduce image blur as we move in the environment. In non-primate mammals, this behaviour is initiated by retinal output neurons called ON-type direction-selective ganglion cells (ON-DSGCs), which detect the direction of image motion and transmit signals to brainstem nuclei that drive compensatory eye movements. However, in primates, ON-DSGCs have not yet been identified in the retina, raising the possibility that this reflex is mediated by cortical visual areas. Here, we mined single-cell RNA transcriptomic data from primate retina to identify a candidate ON-DSGC. We then combined two-photon calcium imaging, molecular identification, and morphological analysis, to reveal a population of ON-DSGCs in the macaque retina. The morphology, molecular signature, and GABAergic mechanisms that underlie direction selectivity in primate ON-DSGCs are highly conserved with lower mammals. We further show that the human retina contains a homologous cell type. The presence of ON-DSGCs in primates highlights the need to examine the contribution of subcortical retinal mechanisms to normal and aberrant gaze stabilisation in the developing and mature visual system.
This dataset contains the raw data from the paper: "An ON-type direction selective ganglion cell in primate retina".
The data are from the following experiments:
- Immunohistochemistry (IMHC): Pieces of macaque retina were stained for BNC2, RBPMS, and FOXP2 to analyze the density and proportion of pRGC10s and pRGC16s (Figure 1d-e), and their mosaic properties (Extended Data Fig. 1). IMHC was performed after calcium imaging to determine the molecular identity of recorded cells (macaque; Figure 2, mouse; Extended Data Fig. 5.). Candidate human On-DSGCs were labeled with BNC2 and RPBMS (Figure 4). Additional antibody validation was also performed (Extended Data Fig. 7).
- Calcium imaging: Calcium responses to light stimuli were recorded from the ganglion cell layer in ex vivo macaque (Figure 2, Figure 3e-h) and mouse retinas (Extended Data Fig. 5). Stimuli include a bar drifting in 8 directions (2.24 degrees/s for macaque; 8 degrees/s for mouse). A subset of macaque direction selective cells were centred in the scan field and probed with bright bars moving in the preferred and null directions at a range of velocities (0.57-9 degrees/s) (Extended Data Fig. 4). One centred cell was also stimulated with bright spots of increasing diameter (25-750 μm) (Extended Data Fig. 4).
- DiI filling: Iontophoretically filling cells with DiI in macaque tissue that was pre-labelled with BNC2. We then analysed their morphology (Figure 1f), stratification, and relationship with starburst amacrine cell processes (Figure 3a-d).
- In situ hybridization (RNAscope): Used to validate single cell RNA sequencing data that suggests pRGC10 may contain multiple subtypes. One putative pRGC10 subtype shows expression of FSTL4 (Extended Data Fig. 2d-e).
See the manuscript methods for further details on experimental design and analyses. See the readme.html files included in each figure's folder for more information on the datasets.
Description of the data and file structure
The dataset is organized in folders according to Figure or Extended Data Figure (EDF) number. A "readme" .html file in each .zip file contains additional information on how the data are organized. The content of each zip file is summarized below:
Figure_1 - BNC2 is a putative marker of macaque ON-DSGCs
Raw .czi confocal image files (supporting Fig. 1d-e)
Figure_2 - pRGC10 cells are direction-selective
Igor .pxp files containing raw calcium imaging data from macaque retina
Raw .tif image files showing 2P calcium imaging scan fields registered to IMHC
. zip files containing Image J ROIsets delineating cells in each scan field
Figure_3 - GABAergic inhibition is required for directional tuning of primate ON-DSGCs
Raw .czi and .tif image files of cells used for stratification analysis (supporting Fig. 3d)
Figure_4 - A candidate ON-DSGC in human retina
Raw .czi image files (supporting Fig. 4b)
EDF_1 - Macaque pRGC10 mosaic properties suggest the presence of multiple mosaics
Raw/processed image files (.czi & .tif) and Image J .roi files (supporting EDF 1b-f).
EDF_2 - pRGC10 cells are comprised of molecular sub-clusters
Raw .czi image files supporting RNAscope analysis (EDF 2d-e)
EDF_3 - BNC2+ RGCs are concentrated on the horizontal midline
Raw .zvi image files
EDF_4. ON-DSGCs show ON responses to spot and bar stimuli and are tuned to slower velocities
Readme file only pointing to location of relevant data files.
EDF_5 - Identification of mouse ON-DSGCs with calcium imaging and post-hoc immunostaining
Igor .pxp files containing raw calcium imaging data from mouse retina
Raw .tif image files showing 2P calcium imaging scan fields registered to IMHC
. zip files containing Image J ROIsets delineating cells in each scan field
EDF_6 - Post-hoc molecular identification of a macaque ON-DSGC treated with gabazine.
Readme file with details of .tif image files showing 2P calcium imaging scan fields registered to IMHC
EDF_7 - Specificity of BNC2 antibodies.
Raw .czi image files supporting EDF 7a-b, d-f
EDF_8 - BNC2+ cells with bistratified morphology
Raw .czi confocal image files
Usage notes
- Images are .czi or .tif files, which can both be read in FIJI/ImageJ.
- Calcium imaging responses are in a .pxp file which can be read by Igor Pro
- The "readme" files are .html and can be opened with any web browser.
Other data
Publicly available single cell RNA sequencing data:
- GEO:GSE118480 (macaque)
- GEO:GSE148077 (human)
- GEO:GSE137400 (mouse)