A cell atlas of the chick retina based on single-cell transcriptomics
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, United States
Figures
Figure 1 with 1 supplement
Datasets used to generate a chick retinal atlas.
(A) Cross-section of chick retina stained with NeuroTrace to mark somata. The retina consists of three cellular layers: outer nuclear layer (ONL), inner nuclear layer (INL), and ganglion cell layer …
Figure 1—figure supplement 1
Quality control metrics for datasets used in this paper .
(A) Expression of housekeeping genes (Eisenberg and Levanon, 2013) in E18 retina. Clusters generated from initial unsupervised analysis are shown; following division into classes (Figure 1D,E), each …
Figure 2
Introduction of tags and reporters to specific loci using eCHIKIN.
(A) The eCHIKIN method. In ovo electroporation of Cas9/guideRNA ribonucleoprotein complexes edits the gene specified by the guide RNA, inserting a sequence encoding HA tag, GFP, or CRE. To identify …
Figure 3 with 2 supplements
Classification and characterization of photoreceptors (PRs).
(A) Clustering of E18 PRs displayed in UMAP. Identities of each cluster are indicated to the right. (B) Dot plots showing expression of selected genes expressed in all or subsets of PRs. In this and …
Figure 3—figure supplement 1
Frequency distribution of photoreceptors and comparison of E12 and E18 data .
(A) Frequency distribution of photoreceptor (PR) types. Cluster numbers are from Figure 3A. (B, C) Clustering of PRs from E12 and E18 together and visualized in the same UMAP, showing that the …
Figure 3—figure supplement 2
Regional distribution of developing photoreceptor cell types.
(A–D) In situ hybridization of E12 retina (A,B) and E20 retina (C,D) for OPN1LW and ARGHAP18. (E–P) Central and peripheral staining of SLIT1 (E–G), STRA6 (H–J), OPN1LW (K–M), ARGHAP18 (N–P) at E16. …
Figure 4 with 1 supplement
Classification and characterization of horizontal cells (HC).
(A) Clustering of E18 HCs viewed by UMAP. (B) Dot plots showing expression of selected genes expressed in all or subsets of HCs. Numbers correspond to clusters in A. Dendrogram above dots shows …
Figure 4—figure supplement 1
Frequency and regional distributions of horizontal cell types.
(A) Frequency distribution of horizontal cells (HCs). Cluster numbers are from Figure 4A,B. (B–M) In situ hybridization for OXT and IPCEF1 in central and peripheral retina at E14, E18, and E20. Bar …
Figure 5 with 1 supplement
Classification and characterization of bipolar cells (BCs).
(A) Clustering of E18 BCs visualized by UMAP. (B) Dot plots showing expression of selected genes expressed in all or subsets of BCs. Numbers correspond to clusters in A. Dendrogram above dots shows …
Figure 5—figure supplement 1
Frequency distribution and laminar position of bipolar cell types.
(A) Frequency distribution of bipolar cells (BCs). Cluster numbers are from Figure 5A,B. (B–O) In situ hybridization or immunostaining of E16 retina with indicated probes. (B,C) GRIK1 (B) and TRPM1 …
Figure 6 with 2 supplements
Classification and characterization of amacrine cells (ACs).
(A) Clustering of E18 ACs using UMAP. (B) Dot plots showing expression of the housekeeping gene, GAPDH; pan-AC genes PAX6 and SLC32A1; genes diagnostic of GABAergic ACs (SLC6A1, GAD1, GAD2) and …
Figure 6—figure supplement 1
Frequency distribution and morphological analysis of amacrine cell types.
(A) Frequency distribution of amacrine cells (ACs). Cluster Numbers are from Figure 6A,B. B–D, Immunostaining for NMB in AC17 (B), CHODL in AC40 (C), NPY in AC52 (D). (E–H) Double color in situ …
Figure 6—figure supplement 2
Molecular and morphological analysis of key amacrine cell types.
(A) Violin plots showing differentially expressed genes in two clusters of E18 chick starburst ACs which are characterized by similar expression of CHAT and ISL1. (B) Dot plots of SLC17A8 (VGLUT3), S…
Figure 7 with 2 supplements
Classification and characterization of RGCs.
(A) Clustering of E16 RGCs using UMAP. (B) Dot plots showing expression of selected genes expressed in all or subsets of RGCs. Numbers correspond to clusters in A. Dendrogram above dots shows …
Figure 7—figure supplement 1
Frequency distribution and morphological analysis of retinal ganglion cell types.
(A) Frequency distribution of RGCs. Cluster numbers are from Figure 7A,B. (B–I) In situ hybridization of E16 retina for MODX1 in GC34 (B), LOC419389 in GC32 (C), ZIC1 in GC3 (D), ETV1 in GC15 or 21 …
Figure 7—figure supplement 2
Markers expressed and co-expressed by key retinal ganglion cell types.
Double-color in situ hybridization on E16 retina for RGC markers. Blue, DAPI.
Figure 8 with 3 supplements
Transcriptomic map of topographic position in Müller glia.
(A) Clustering of E18 MGs using UMAP. Inset shows relationship between clusters and retinal position. (B,C) Violin (B) and feature (C) plots of genes differentially expressed among MG clusters. B …
Figure 8—figure supplement 1
Regional distributions of Müller glial cell positional variants.
(A–F) In situ hybridization for WIF1 (A), CHRDL1(B) at E16, FOXG1 (C), FOXI2 (D) at E14, PSCA (E), TMEM123 (F) at E16. Sections were co-stained with anti-glutamate synthetase (anti-GS), showing that …
Figure 8—figure supplement 2
Co-expression of positional markers in Müller glia.
Co-expression in E18 (A) and E12 (B) retina. The x-axis and y-axis are the expression level of the marker genes, and each dot represents one Müller glial cell. Histogram plots on the top and right …
Figure 8—figure supplement 3
Developmental trajectories of Müller glial cell variants.
(A) Feature plots with a set of positional genes at E12 (see Figure 8C for expression at E18). (B) In situ hybridization for FGF8 and PSCA at E16, showing co-expression of FGF8 and PSCA at the high …
Figure 9 with 1 supplement
Developmental trajectory of oligodendrocytes.
(A) Clustering of E18 oligodendrocytes viewed in UMAP. (B) Dot plots showing expression of selected genes expressed in all or subsets of oligodendrocytes. Numbers correspond to clusters in A. (C-K) …
Figure 9—figure supplement 1
Frequency distribution and molecular analysis of oligodendrocyte variants.
(A) Frequency distribution of oligodendrocytes. Cluster Numbers are from Figure 9A,B. (B,C) Feature plots showing expression of oligodendrocyte-characteristic genes that have been studied in mammals …
Figure 10
Conserved transcriptomic identity of cell classes in mammals and chicks.
(A) UMAP visualization of pooled cells from chick, mouse, macaque following unsupervised clustering. Colors distinguish classes identified by reference to canonical markers (C) and labels previously …
Figure 11 with 2 supplements
Conserved transcriptomic identity of photoreceptor (PR), horizontal (HC), and bipolar cell (BC) types in mammals and chicks.
Consensus dendrogram tree for PR (A), HC (B), and BC (C) types from chick, mouse, macaque, and human single-cell dataset. In C, ON and OFF types are globally separated by a dotted line, but three …
Figure 11—figure supplement 1
Cross-species comparisons of amacrine cell types.
(A) UMAP visualization of pooled amacrine cells (ACs) from chick, mouse, macaque, and human retina following unsupervised clustering. (B) The same as A, but colors code for species. (C) Relationship …
Figure 11—figure supplement 2
Cross-species comparisons of retinal ganglion cell types.
(A) UMAP visualization of pooled RGCs from chick, mouse, macaque and human retina following unsupervised clustering. (B) The same as A, but colors code for species. (C) Relationship of clusters from …
Figure 12
Down-sampling test of chick bipolar cells (BCs), amacrine cells (ACs), and RGCs.
Graphs show the number of cell clusters identified when using 10–90% of total cells, 10 repeats each (Mean ± SD). (A) BCs. (B) ACs. (C) RGCs.
Tables
Table 1
Numbers of cell types in mouse, primate (Macaque), and chick retina.
| Cell class | Mouse | Macaque* | Chick (mature) | Chick (developing or topographic) |
|---|---|---|---|---|
| Photoreceptors | 3 | 4 | 8 | 4 |
| Horizontal cells | 1 | 2 | 4 | 1 |
| Bipolar cells | 15 | 12 | 22 | - |
| Amacrine cells | 63 | 34 | 59 | - |
| RGCs | 46 | 18 | 41 | - |
| Müller glia | 1 | 1 | 1 | 6† |
| Oligodendrocytes | 0 | 0 | 1 | 4 |
| Astrocytes | 1 | 1 | 0 | 0 |
| Total | 129 | 72 | 136 | 15† |
-
Mouse: Macosko et al., 2015; Shekhar et al., 2016; Tran et al., 2019; Yan et al., 2020a.
Macaque: Peng et al., 2019.
-
*Peripheral retinal types plus foveal types not found in periphery.
†We found six positional variants of a single MG type, so the number of MG groups is 6, not 5 and the total number of groups is 150 (136+14) not 151 (136+15).
Key resources table
| Reagent type (species) or resource | Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Genetic reagent (Gallus gallus) | GRCg6a | International Chicken Genome Consortium | GCF_000002315.5 | |
| Species | Fertilized chicken eggs (specific pathogen free) | Charles River Laboratories | Cat# 10100326 | |
| Sequenced-based reagent | Sequences of probes used for in situ hybridization | IDT | Supplementary file 1 in this study | |
| Sequenced-based reagent | Sequences of homology arms used to generate eCHIKIN probes | IDT, this study | Supplementary file 2 in this study | |
| Sequenced-based reagent | Alt-R CRISPR-Cas9 crRNA (specific to each gene) | IDT | Supplementary file 2 in this study | |
| Recombinant DNA reagent | pXL-BacII-CAG-Zeocin-3xF2A | Martell et al., 2016 (doi:10.1038/nbt.3563) | ||
| Recombinant DNA reagent | pCAG-PBorf | Yamagata and Sanes, 2012 (doi:10.1523/JNEUROSCI.3193-12.2012) | ||
| Recombinant DNA reagent | pXL-BacII-CAG-mCherry | This study | ||
| Recombinant DNA reagent | pXL-BacII--loxP-STOP-loxP-Venus | This study | ||
| Recombinant DNA reagent | pXL-BacII-CAG-Venus | Yamagata and Sanes, 2012 (doi:10.1523/JNEUROSCI.3193-12.2012) | ||
| Recombinant DNA reagent | pCAG-Cre:GFP | Addgene | Addgene#13776 | |
| Antibody | Anti-chicken Thy1 (Mouse monoclonal) | BSJ-1 (French and Jeffrey, 1986, doi:10.1002/jnr.490160304) | 0.01 µ /ml for cell purification | |
| Antibody | Anti-Calbindin (Rabbit polyclonal) | Swant | Cat# CB-38a; RRID:AB_10000340 | IF(1/1000) |
| Antibody | Anti-GFP (Rabbit polyclonal) | Millipore | Cat# AB3080P; RRID:AB_2630379 | IF(1/1000) |
| Antibody | Anti-Brn3a (Mouse monoclonal) | Millipore | Cat# MAB1585; RRID:AB_94166 | IF(1/1000) |
| Antibody | Anti-Calretinin (Rabbit polyclonal) | Millipore | Cat# AB5054; | IF(1/1000) |
| RRID:AB_2068506 | ||||
| Antibody | Anti-Calbindin (Rabbit polyclonal) | Swant | Cat# CB38; RRID:AB_10000340 | IF(1/1000) |
| Antibody | Anti-Protein kinase C- α (Rabbit polyclonal) | Sigma | Cat# P4334 | IF(1/10000) |
| Antibody | Anti-VSX2 (Rabbit polyclonal) | GeneTex | Cat# GTX114143 | IF(1/1000) |
| Antibody | Anti-HA tag (Rat monoclonal) | Roche | Clone name: 3F10 | IF(1/1000) |
| Antibody | Anti-Satb1 (Rabbit polyclonal) | Abcam | Cat# ab109122; RRID:AB_10862207 | IF(1/1000) |
| Antibody | Anti-Satb2 (Mouse monoclonal) | Abcam | Cat# ab51502; RRID:AB_882455 | IF(1/1000) |
| Antibody | Anti-Neuropeptide Y (Rabbit polyclonal) | Abcam | Cat# ab10980 | IF(1/1000) |
| Antibody | Anti-AP2A (Mouse monoclonal) | Developmental Studies Hybridoma Bank | Clone name: 3B5 | IF(1/100) |
| Antibody | Anti-AP2B (Mouse monoclonal) | Developmental Studies Hybridoma Bank | Clone name: 2A4 | IF(1/100) |
| Antibody | Anti-OTX1 (Mouse monoclonal) | Developmental Studies Hybridoma Bank | Clone name: 5F5 | IF(1/100) |
| Antibody | Anti-SOX5 (Mouse monoclonal) | Developmental Studies Hybridoma Bank | Clone name: 1C12 | IF(1/100) |
| Antibody | Anti-PAX6 (Mouse monoclonal) | Developmental Studies Hybridoma Bank | Clone name: PAX6 | IF(1/100) |
| Antibody | Anti-NMB (Mouse monoclonal) | Developmental Studies Hybridoma Bank | Clone name: NMB1 | IF(1/10) |
| Antibody | Anti-STRA6 (Mouse polyclonal) | This study | IF (1:1000) | |
| Antibody | Anti-TPBGL (Mouse polyclonal) | This study | IF (1:500) | |
| Antibody | Anti-SLC6A4 (Mouse polyclonal) | This study | IF (1:200) | |
| Antibody | Anti-chicken choline acetyltransferase (Rabbit polyclonal) | Johnson and Epstein, 1986 (doi:10.1111/j.1471-4159.1986.tb13064.x) | IF (1:1000) | |
| Antibody | Anti-chicken glutamate synthetase (Rabbit polyclonal) | Linser and Moscona, 1979 (doi: 10.1073/pnas.76.12.6476) | IF (1:1000) | |
| Commercial assay or kit | Papain Dissociation System, Without EBSS | Worthington | Cat# LK003160 | |
| Commercial assay or kit | Chromium Single Cell 30Library and Gel Bead Kit v2, 10X Genomics Cat#120237 16rxns | 10 X Genomics | Cat# 120237 | |
| Chemical compound, drug | Goat anti-mouse IgG conjugated magnetic beads | Miltenyi Biotec | Cat# 484–02 | |
| Chemical compound, drug | Alt-R CRISPR-Cas9 tracrRNA | IDT | Cat# 1072533 | |
| Chemical compound, drug | Alt-R S.p. Cas9 Nuclease V3 | IDT | Cat# 1081058 | |
| Chemical compound, drug | Alt-R Cas9 Electroporation Enhancer | IDT | Cat# 1075915 | |
| Chemical compound, drug | Alt-R HDR Enhancer | IDT | Cat# 1081072 | |
| Chemical compound, drug | Fast Green FCF | Sigma-Aldrich | Cat# F7252 | |
| Commercial assay or kit | TSA Cyanine 3 Plus Evaluation Kit | Perkin Elmer | Cat# NEL744E001KT (FP1170) | |
| Commercial assay or kit | TSA Fluorescein Plus Evaluation Kit | Perkin Elmer | Cat# NEL741E001KT (FP1168) | |
| Chemical compound, drug | Anti-Digoxigenin-POD, Fab fragments | Roche | Cat# 11207733910 | |
| Commercial assay or kit | EconoTaq PLUS GREEN 2X Master Mix | Lucigen | Cat# 30033–1 | |
| Commercial assay or kit | CIAquick-Gel Extraction Kit | Oiagen | Cat# 28704 | |
| Commercial assay or kit | MiniMACS Separation Unit | Miltenyi Biotec | Cat# 421–02 | |
| Other | MACS Multistand | Miltenyi Biotec | Cat# 423–03 | |
| Other | Type WHM large cell separation columns | Miltenyi Biotec | Cat# 422–02 | |
| Other | BTX 830 | BTX | Cat# 45–0662 | |
| Other | Genetrode | BTX | Cat# 45–0116 | |
| Software, algorithm | ImageJ (Fiji) Version 2.1.0 | Fiji | https://imagej.net/Fiji | |
| Software, algorithm | R 3.6.2 | The R foundation | https://www.r-project.org/ | |
| Software, algorithm | RStudio 1.3.1056 | Rstudio | https://rstudio.com | |
| Software, algorithm | Adobe Photoshop 20.0.9 release | Adobe | https://www.adobe.com |
Additional files
-
Supplementary file 1
Sequences of probes used for in situ hybridization.
- https://cdn.elifesciences.org/articles/63907/elife-63907-supp1-v2.xlsx
-
Supplementary file 2
Sequences of homology arms used to generate eCHIKIN probes.
- https://cdn.elifesciences.org/articles/63907/elife-63907-supp2-v2.xlsx
-
Supplementary file 3
Basic quality measures of each cluster.
- https://cdn.elifesciences.org/articles/63907/elife-63907-supp3-v2.zip
-
Transparent reporting form
- https://cdn.elifesciences.org/articles/63907/elife-63907-transrepform-v2.docx
