| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| CD73-PE antibody | Miltenyi Biotec | Catalog: 130-102-616 |
| Anti-PE microbeads | Miltenyi Biotec | Catalog: 130-105-639 |
| CD90.1 microbeads | Miltenyi Biotec | LOT: 130-094-523 |
| papain | Worthington Biochemical | Catalog: LS003126 |
| Critical commercial assays | ||
| Chromium Single Cell 3′ Library & Gel Bead Kit v2, 16 rxns | 10X Genomics | Cat# PN-120237 |
| Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3, 16 rxns | 10X Genomics | Cat# PN-1000075 |
| Chromium Next GEM Single Cell 3ʹ Kit v3.1, 16 rxns | 10X Genomics | Cat# PN-1000268 |
| Deposited data | ||
| Raw and analyzed data | Yan et al.12 | GSE149715 |
| Raw and analyzed data | Shekhar et al.11 | GSE81904 |
| Raw and analyzed data | Tran et al.9 | GSE133382 |
| Raw and analyzed data | Jacobi et al.13 | GSE201254 |
| Raw and analyzed data | Ma et al.,15 | GSE254587 |
| Raw and analyzed data | Benhar et al.14 | GSE199317 |
| Raw and analyzed data | This paper | GSE243413 |
| Analyzed data | This paper | https://doi.org/10.5281/zenodo.10815031 |
| The landing page of the MRCA | This paper | https://rchenlab.github.io/resources/mouse-atlas.html |
| Interactive visualization on CELLxGENE | This paper | https://cellxgene.cziscience.com/collections/a0c84e3f-a5ca-4481-b3a5-ccfda0a81ecc |
| Interactive visualization on the data portal at Baylor College of Medicine | This paper | https://mouseatlas.research.bcm.edu |
| Interactive visualization on UCSC Cell Browser | This paper | https://retina.cells.ucsc.edu |
| Interactive visualization on the Broad Single Cell Portal: Full atlas | This paper | https://singlecell.broadinstitute.org/single_cell/study/SCP2560 |
| Interactive visualization on the Broad Single Cell Portal: BC subclass | This paper | https://singlecell.broadinstitute.org/single_cell/study/SCP2559 |
| Interactive visualization on the Broad Single Cell Portal: AC subclass | This paper | https://singlecell.broadinstitute.org/single_cell/study/SCP2557 |
| Interactive visualization on the Broad Single Cell Portal: RGC subclass | This paper | https://singlecell.broadinstitute.org/single_cell/study/SCP2558 |
| Software and algorithms | ||
| scvi-tools v1.0.4 | Gayoso et al.38 | https://scvi-tools.org |
| R v4.3.2 | N/A | https://www.r-project.org |
| Seurat v4.4.0 | Hao et al.39 | https://satijalab.org/seurat |
| 10x Genomics CellRanger v7.0.1 | Zheng et al.40 | https://www.10xgenomics.com |
| 10x Genomics Mouse mm10 v2020-A | 10X Genomics | https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-mm10-2020-A.tar.gz |
| Scanpy v1.9.1 | Wolf et al.41 | https://scanpy.readthedocs.io/en/stable |
| scPred v1.9.2 | Alquicira-Hernandez et al.42 | https://github.com/powellgenomicslab/scPred |
| DoubletFinder v2.0.4 | McGinnis et al.43 | https://github.com/chris-mcginnis-ucsf/DoubletFinder |
| DropletUtils v1.22.0 | Lun et al.44 | https://bioconductor.org/packages/release/bioc/html/DropletUtils.html |
| SeuratDisk v0.0.0.9021 | N/A | https://github.com/mojaveazure/seurat-disk |
| SoupX v1.6.2 | Young et al.45 | https://github.com/constantAmateur/SoupX |
| Snakemake v7.32.4 | Molder et al.46 | https://github.com/snakemake/snakemake |
| dropkick v1.2.8 | Heiser et al.47 | https://github.com/KenLauLab/dropkick |
| CellQC v0.0.7 | This paper | https://github.com/lijinbio/cellqc |
| Analysis code | This paper | https://github.com/RCHENLAB/MouseRetinaAtlas_manuscript |
| Other | ||
| Illumina Novaseq 6000 | Illumina | N/A |
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