Key resources table
| Reagent or Resource | Source | Identifier |
|---|---|---|
| Antibodies | ||
| anti-CRX A-9 (for ChIP-seq) | Santa Cruz Biotechnology | sc-377138 |
| anti-CRX M02 (for Western Blot) | Abnova Corp. | H00001406-M02 |
| anti-HDACl H51 | Santa Cruz Biotechnology | sc-7872 |
| anti-mCAR | MilliporeSigma | MilliporeSigma |
| anti-RHO | MilliporeSigma | O4886 |
| anti-RXRG | Santa Cruz Biotechnology | sc-555 |
| IRDye® 680RD Goat anti-Rabbit IgG Secondary Antibody | LI-COR | 926–68071 |
| IRDye® 800CW Goat anti-Mouse IgG Secondary Antibody | LI-COR | 926–32210 |
| Chemicals | ||
| Atropine sulfate solution | Bausch and Lomb | NDC 24208-825-55 |
| Chameleon® Duo Pre-stained Protein Ladder | LI-COR | 928–60000 |
| Dithiothreitol (DTT) | Bio-Rad Laboratories | 1610611 |
| Exonuclease I (E. coli) | New England Biolabs | M0293S |
| Gibco™ Dulbecco’s Modified Eagle Medium | ThermoFisher Scientific | 11965084 |
| Gibco™ Fetal Bovine Serum | ThermoFisher Scientific | 16000044 |
| Glutathione Sepharose 4B resin | Cytiva | 17075601 |
| Isopropyl-β-D-thiogalactopyranoside (IPTG) | ThermoFisher Scientific | BP1755–10 |
| Molecular Biology Grade Water | Corning® | 46–000-CM |
| Penicillin-Streptomycin | ThermoFisher Scientific | 15140122 |
| Phosphate Buffered Saline | Corning® | 46–013-CM |
| Roche cOmplete™, Mini Protease Inhibitor Cocktail | MilliporeSigma | 11836153001 |
| SeeBlue™ Plus2 Pre-stained Protein Standard | Invitrogen | LC5925 |
| Triton X-100 | Sigma-Aldrich | T9284 |
| TRIzol™ Reagent | Invitrogen | 15596026 |
| VECTASHIELD® HardSet™ Antifade Mounting Medium with DAPI | Vector Laboratories | H-1500–10 |
| Critical commercial assays | ||
| Amicon Ultra-0.5 Centrifugal Filter Unit | Millipore | UFC500324 |
| Dual-Luciferase Reporter Assay System | Promega | E1910 |
| GST SpinTrap™ | Cytiva | 28952359 |
| iScript™ Reverse Transcription Supermix | Bio-Rad Laboratories | 1708841 |
| MEGAshortscript™ T7 Transcription Kit | Thermo Fisher Scientific | AM1354 |
| MinElute PCR Purification Kit | QIAGEN | 28006 |
| NE-PER Nuclear and Cytoplasmic Extraction Reagents | Thermo Scientific | 78833 |
| Novex™ WedgeWell™ 12% Tris-Glycine Mini Protein Gels | Invitrogen | XP00122BOX |
| NuPAGE™ 4 to 12%, Bis-Tris Mini Protein Gels | Invitrogen | NP0322BOX |
| Phusion® High-Fidelity PCR Master Mix with HF Buffer | New England Biolabs | M0531S |
| SsoFast™ EvaGreen® Supermix with Low ROX | Bio-Rad Laboratories | 1725211 |
| Deposited data | ||
| Spec-seq - in vitro | This study | GEO |
| ChIP-seq - mouse retina | This study | GEO |
| RNA-seq - mouse retina | This study | GEO |
| RNA-seq - mouse retina | Aldiri et al. 201739 | GEO: GSE87064 |
| Equipment | ||
| Bioanalyzer | Agilent | 2100 |
| Leica DB5500 microscope | Leica | DB5500 |
| Mini Blot Module | Invitrogen | B1000 |
| Odyssey® CLx and Fc Imaging Systems | LI-COR Biosciences | CLX 1894 |
| Visual electrodiagnostic system | LKC Technologies | UTAS-E3000 |
| Experimental models: Cell lines | ||
| HEK293T | ATCC | CRL-3216™ |
| Experimental models: Organisms/strains | ||
| Mus musculus/C57BL/6J | The Jackson Laboratory | Cat #000664 |
| Oligonucleotides | ||
| Listed in Supplementary Table S2 | ||
| Software and algorithms | ||
| bedtools (v2.27.1) | Quinlan and Hall, 201097 | https://bedtools.readthedocs.io/en/latest/ |
| Bowtie2 (v 2.3.4.1) | Langmead and Salzberg, 201294 | https://bowtie-bio.sourceforge.net/bowtie2/index.shtml |
| BSgenome (v 1.58.0) | Pages, 2020108 | https://bioconductor.org/packages/BSgenome |
| Clustal Omega | Goujon et al. 2010118; Sievers et al. 2011119 | https://www.ebi.ac.uk/Tools/msa/clustalo/ |
| clusterProfiler (v4.0.5) | Yu et al., 2012113; Wu et al., 2021114 | https://bioconductor.org/packages/clusterProfiler |
| DAVID (v6.8) | Sherman et al., 2022112 | https://david.ncifcrf.gov/ |
| deeptools (v3.0.0) | Ramirez et al., 201698 | https://deeptools.readthedocs.io/en/develop/ |
| DEseq2 (v1.30.1) | Love et al., 2014104 | https://bioconductor.org/packages/DESeq2 |
| DiffBind (v3.0.15) | Stark and Brown, 2011102; Ross-Innes et al., 2012103 | https://bioconductor.org/packages/DiffBind |
| fastcluster (v1.1.26) | Müllner, 2013107 | http://danifold.net/fastcluster.html |
| FastQC (v0.11.5) | 93 | http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ |
| GraphPad Prism 8 | GraphPad Software | https://www.graphpad.com/scientific-software/prism/ |
| GREAT (v4.0.4) | McLean et al., 2010105 | http://great.stanford.edu/public/html/ |
| HOMER (v4.8) | http://homer.ucsd.edu/homer | |
| IDR framework (v2.0.4) | Li et al., 2011101 | https://github.com/nboley/idr |
| IGV Web App | Robinson, Thorvaldsdóttir, Winckler et al., 201199 | https://igv.org/ |
| Jalview (v2.11.1.7) | Waterhouse et al., 2009120 | https://www.jalview.org/ |
| kallisto (v0.46.2) | Bray et al., 2016110 | https://github.com/pachterlab/kallisto |
| logomaker (v0.8) | Tareen and Kinney, 2020121 | https://logomaker.readthedocs.io/en/latest/ |
| MACS2 (v2.1.1.20160309) | Zhang et al., 2008100 | https://github.com/macs3-project/MACS |
| matplotlib (v3.5.1) | Hunter, 2007122 | https://matplotlib.org/ |
| MEME Suite (v5.0.4) | Bailey et al., 2015109 | https://meme-suite.org/meme/index.html |
| org.Mm.eg.db (v3.12.0) | Carlson, 2019115 | https://bioconductor.org/packages/org.Mm.eg.db |
| pandas (v1.4.2) | Reback, 2022123 | https://pandas.pydata.org/ |
| Picard (v2.21.4) | Picard toolkit96 | http://broadinstitute.github.io/picard/ |
| python (v3.9.12) | Rossum and Drake, 1995124 | https://docs.python.org/3Zreference/ |
| R (v4.0.3) | R Core Team 2020 | |
| rGREAT (v1.19.2) | Gu and Huebschmann, 2022106 | https://bioconductor.org/packages/rGREAT |
| samtools (v1.9) | Li et al., 200995 | http://www.htslib.org/ |
| scikit_posthocs (v0.7.0) | Terpilowski, 2019117 | https://scikit-posthocs.readthedocs.io/en/latest/ |
| scipy (v1.8.1) | Virtanen et al., 2020116 | https://scipy.org/ |
| seaborn (v0.11.2) | Waskom, 2021125 | https://seaborn.pydata.org/ |
| Trim Galore (v0.6.1) | Krueger et al., 202392 | https://github.com/FelixKrueger/TrimGalore |
| tximport (v1.18.0) | Soneson, Love and Robinson, 2015111 | https://bioconductor.org/packages/tximport |