KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
|
| ||
| Antibodies | ||
|
| ||
| Goat anti-Brn3 (1:50) | Santa Cruz Biotechnology | Cat#sc6026; RRID: AB_673441 |
| Mouse anti-Brn3a (1:200) | Millipore | Cat#MAB1585; RRID: AB_94166 |
| Mouse anti-Otx2 (1:200) | Santa Cruz Biotechnology | Cat#sc-514195 |
| Rabbit anti-calbindin D-28K (1:2000) | Millipore | Cat#PC253L; RRID: AB_213554 |
| Mouse anti-Rxrγ (1:250) | Santa Cruz Biotechnology | Cat#sc-365252; RRID: AB_10850062 |
| Rabbit anti-recoverin (1:2000) | Millipore | Cat#AB5585; RRID: AB_2253622 |
| Goat anti-Vsx2/Chx10 (1:500) | gift from Dr. Edward M. Levine | N/A |
| Sheep anti-Vsx2/Chx10 (1:500) | Exalpha Biologicals | Cat#X1180P; RRID: AB_2314191 |
| Mouse anti-Rhodopsin (1:200) | Thermo Fisher Scientific | Cat#MA5–11741; RRID: AB_10980983 |
| Rabbit anti-Lhx2 (1:500) | Abcam | Cat# ab184337, RRID: AB_2916270 |
| Mouse anti-Cralbp (1:500) | Novus | Cat# NB100–74392, RRID: AB_2253681 |
| Mouse anti AP-2alpha (1:500) | Santa Cruz Biotechnology | Cat#sc-12726, RRID: AB_667767 |
| Mouse anti-PCNA (1:2000) | Sigma-Aldrich | Cat#P8825, RRID: AB_477413 |
| Rabbit anti-pH3 (Ser10) (1:250) | Millipore | Cat#06–570; RRID: AB_310177 |
| Rabbit anti-Foxp1 (1:2000) | Abcam | Cat#ab16645; RRID: AB_732428 |
| Rabbit anti-H3K27me3 | Millipore | Cat#07–449; RRID: AB_310624 |
| Sheep anti-Onecut2 (1:100) | R&D Systems | Cat#AF6294; RRID: AB_10640365 |
| Donkey anti-rabbit 488 (1:400) | Thermo Fisher Scientific | Cat#A-21206, RRID: AB_2535792 |
| Donkey anti-rabbit 555 (1:400) | Thermo Fisher Scientific | Cat#A31572; RRID: AB_162543 |
| Donkey anti-mouse 488 (1:400) | Thermo Fisher Scientific | Cat#A-21202, RRID: AB_141607 |
| Donkey anti-mouse 555 (1:400) | Thermo Fisher Scientific | Cat#A-31570, RRID: AB_2536180 |
| Donkey anti-sheep 555 (1:400) | Thermo Fisher Scientific | Cat#A-21436, RRID: AB_2535857 |
| Donkey anti-goat 488 (1:400) | Thermo Fisher Scientific | Cat#A-11055, RRID: AB_2534102 |
|
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| Chemicals, peptides, and recombinant proteins | ||
|
| ||
| DNAse I | Sigma-Aldrich | Cat#D4513 |
| Liberase | Sigma-Aldrich | Cat#5401119001 |
| RBC lysis buffer | eBioscience | Cat#00–4333-57 |
| Tamoxifen | Sigma-Aldrich | Cat#T5648 |
|
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| Critical commercial assays | ||
|
| ||
| Click-iT plus EdU Imaging Kits | Thermo Fisher Scientific | Cat#C10637 |
| RNeasy Plus Mini Kit | Qiagen | Cat#74134 |
| CUT&RUN Assay Kit | Cell Signaling | Cat#86652 |
| Spin column Kit for Cut&Run | Cell Signaling | Cat#14209 |
| RNA ScreenTape Assay | Agilent Technologies | Cat#5067–5576, 5067–5577, 5067–5578 |
| D1000 ScreenTape Assay | Agilent Technologies | Cat#5067–5582, 5067–5583 |
| Kapa Library Quant Kit | Kapa Biosystems | Cat#KK4824 |
| NEBNext Ultra II Directional RNA Library Prep Kit for Illumina | New England Biolabs | Cat#E7760 |
| NEBNext rRNA Depletion Kit v2 | New England Biolabs | Cat#E7400 |
| NEBNext UItra II DNA Library Prep Kit for Illumina | New England Biolabs | Cat#E7645 |
| Chromium Single Cell 3′ Library Prep Kit v3 | 10X Genomics | Cat#PN-1000092 |
| Chromium Next GEM Single Cell 3′ Library Prep Kit v3.1 |
10X Genomics | Cat#PN-1000128 |
| NovaSeq XP workflow v1 and v1.5 | Illumina | Cat#20021664, 20043131 |
| NovaSeq S2 and S4 Reagent Kits | Illumina | Cat#20012860, 20028312 |
|
| ||
| Deposited data | ||
|
| ||
| All raw and analyzed data generated for this study | This paper | GEO: GSE202741 |
| Jarid2 cKO scRNA-seq | This paper | GEO: GSE202734 |
| H3K27me3 CUT&RUN from Jarid2 cKO | This paper | GEO: GSE222955 |
| H3K27me3 CUT&RUN from E14.5 and P0 retina | This paper | GEO: GSE202728 |
| Foxp1 cKO RNA-seq | This paper | GEO: GSE202725 |
| Foxp1 cTG scRNA-seq | This paper | GEO: GSE222956 |
| Single Cell-seq of whole retina E11.5 to P5 | Clark et al.11 | GEO: GSE118614 |
| H3K27me3 ChIP-seq from E17.5, P0, and P3 retina | Aldiri et al.29 | GEO: GSE87037 |
|
| ||
| Experimental models: Organisms/strains | ||
|
| ||
| C57BL/6N-Jarid2tm1a(KOMP)Wtsi/Mmucd mice | KOMP Repository | RRID: MMRRC_048262-UCD |
| B6.Cg-Tg(ACTFLPe)9205Dym/J mice | Jackson Laboratory | RRID: IMSR_JAX:005703 |
| Tg(Six3-Cre)69Frty mice | Dr. Yasuhide Furuta (Furuta et al.52) | RRID: IMSR_JAX:019755 |
| Raxtm1.1(cre/ERT2)Sbls/J mice | Dr. Seth Blackshaw (Pak et al.53) | RRID: IMSR_JAX:025521 |
| Foxp1flox/flox mice | Jackson Laboratory (Feng et al.60) | RRID: IMSR_JAX:017699 |
| Foxp1a transgenic mice | Dr. Hui Hu (Wang et al.61) | MGI:5607369 |
|
| ||
| Software and algorithms | ||
|
| ||
| BBTools v38.34 | Bushnell et al.70 | RRID:SCR_016968 |
| cutadapt v1.16 and v2.8 | Martin71 | RRID:SCR_011841 |
| STAR v2.7.0f and v2.7.6a | Dobin et al.72 | RRID:SCR_004463 |
| featureCounts v1.5.1 | Liao et al.73 | RRID:SCR_012919 |
| DESeq2 v1.38.1 | Love et al.74 | RRID:SCR_015687 |
| CellRanger v3.1.0 | 10X Genomics | RRID:SCR_023221 |
| velocyto v0.17.17 | La Manno et al.75 | RRID:SCR_018167 |
| Seurat v4.0.3 | Stuart et al.87 | RRID:SCR_007322 |
| DoubletFinder v2.0.3 | McGinnis et al.76 | RRID:SCR_018771 |
| Monocle3 v1.0.0 | Qiu et al.55 | RRID:SCR_018685 |
| Novoalign v4.02.02 | Novocraft | RRID:SCR_014818 |
| Samtools v1.10 | Danecek et al.77 | RRID:SCR_002105 |
| Macs2 v2.2.7.1 | Zhang et al.78 | RRID:SCR_013291 |
| Fgsea v1.18.0 | Korotkevich et al.79 | RRID:SCR_020938 |
| Gage v2.42.0 | Luo et al.80 | RRID:SCR_017067 |
| GraphPad Prism v9 | GraphPad | RRID:SCR_002798 |
| NIS-Elements v18 | Nikon | RRID:SCR_014329 |