Key resources table.
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Rabbit polyclonal anti-Ibal | Wako | Cat#019-19741; RRID: AB_839504 |
| Goat polyclonal anti-Ibal | Abcam | Cat#ab5076; RRID: AB_2224402 |
| Rat monoclonal anti-CD68 | Bio-Rad | Cat#MCA1957; RRID:AB_322219 |
| Rat monoclonal anti-SIRPα | BD Biosciences | Cat#552371; RRID:AB 394371 |
| Rabbit polyclonal anti-SIRPα | Thermo Fisher | Cat#PA5-19869; RRID:AB 11155968 |
| Rat monoclonal anti-CD47 | BD Biosciences | Cat#555297; RRID:AB 395713 |
| Goat polyclonal anti-CD47 | R&D Systems | Cat#AF1866; RRID:AB 2074942 |
| Chicken polyclonal anti-GFP | Abcam | Cat#ab13970; RRID:AB 300798 |
| Rabbit polyclonal anti-Vglut1 | Synaptic Systems | Cat#135302; RRID:AB 887877 |
| Rabbit polyclonal anti-mouse cone arrestin (mCAR) | Millipore | Cat#AB15282; RRID:AB 11210270 |
| Goat polyclonal anti-PSD95 | Abcam | Cat#ab12093; RRID:AB 298846 |
| Rabbit polyclonal anti-RIBEYE | Synaptic Systems | Cat#192103; RRID:AB_2086775 |
| Rabbit polyclonal anti-secretagogin (SCGN) | BioVendor Laboratory Medicine | Cat#RD181120100; RRID:AB_2034060 |
| Chicken polyclonal anti-Calbindin D-28k | Novus biologicals | Cat#NBP2-50028; N/A |
| Guinea pig polyclonal anti-RBPMS | PhosphoSolutions | Cat#1832-RBPMS; RRID: AB 2395389 |
| Mouse monoclonal anti-AP2 alpha (3B5) | Developmental Studies Hybridoma Bank | Cat#3b5; RRID: AB 528084 |
| Rabbit polyclonal anti-GAPDH | MIllipore | Cat#ABS16; RRID:AB 10806772 |
| Donkey anti-rabbit IgG (H+L) secondary antibody, Alexa Fluor 488 | Jackson ImmunoResearch Labs | Cat#711-545-152; RRID:AB_2313584 |
| Donkey anti-rabbit IgG (H+L) secondary antibody, Alexa Fluor 594 | Jackson ImmunoResearch Labs | Cat#711-585-152; RRID:AB_2340621 |
| Donkey anti-rabbit IgG (H+L) secondary antibody, Alexa Fluor 647 | Jackson ImmunoResearch Labs | Cat#711-605-152; RRID:AB_2492288 |
| Donkey anti-rat IgG (H+L) secondary antibody, Alexa Fluor 488 | Jackson ImmunoResearch Labs | Cat#712-545-150; RRID:AB_2340683 |
| Donkey anti-rat IgG (H+L) secondary antibody, Alexa Fluor 594 | Jackson ImmunoResearch Labs | Cat#712-585-150; RRID:AB_2340688 |
| Donkey anti-rat IgG (H+L) secondary antibody, Alexa Fluor 647 | Jackson ImmunoResearch Labs | Cat#712-605-150; RRID:AB_2340693 |
| Donkey anti-goat IgG (H+L) secondary antibody, Alexa Fluor 488 | Jackson ImmunoResearch Labs | Cat#705-545-003; RRID:AB_2340428 |
| Donkey anti-goat IgG (H+L) secondary antibody, Alexa Fluor 594 | Jackson ImmunoResearch Labs | Cat#705-585-004; RRID:AB_2340432 |
| Donkey anti-goat IgG (H+L) secondary antibody, Alexa Fluor 647 | Jackson ImmunoResearch Labs | Cat#705-605-005; RRID:AB_2340436 |
| Donkey anti-chicken IgY (IgG) (H+L) secondary antibody, Alexa Fluor 488 | Jackson ImmunoResearch Labs | Cat#703-545-155; RRID:AB_2340375 |
| Donkey anti-mouse IgG (H+L) secondary antibody, Alexa Fluor 488 | Jackson ImmunoResearch Labs | Cat#715-545-150; RRID:AB_2340846 |
| Donkey anti-mouse IgG (H+L) secondary antibody, Alexa Fluor 594 | Jackson ImmunoResearch Labs | Cat#715-585-150; RRID:AB_2340854 |
| Critical Commercial Assays | ||
| Plasmid Plus Midi Kit | QIAGEN | Cat#12943 |
| RNAscope Multiplex Fluorescent Reagent Kit v2 Assay | ACD-Biotechne | Cat#323100 |
| RNeasy Mini Kit | QIAGEN | Cat#74104 |
| iScript Reverse Transcription Supermix | BioRad | Cat#170-8840 |
| iTaq Universal SYBR Green Supermix | BioRad | Cat#172-5124 |
| Experimental Models: Organisms/Strains | ||
| Mouse: Cx3cr1+/eGFP: B6.129P-Cx3cr1tm1Litt/J | The Jackson Laboratory | JAX stock #005582 |
| Mouse: Sirpatm1b(EUCOMM)Hmgu | Gift from Beth Stevens (Boston Children’s Hospital) | N/A |
| Mouse: Cd47tm1Fpl | The Jackson Laboratory | JAX stock #003173 |
| Mouse: Six3-Cre | The Jackson Laboratory | Furuta et al., 2000; JAX stock #019755 |
| Mouse: Tnfrsf11a-Cre | Gift from Frederic Geissmann (Memorial Sloan Kettering Cancer Center) | N/A |
| Mouse: Tnfrsf11a-Cre | Gift from Frederic Geissmann (Memorial Sloan Kettering Cancer Center) | N/A |
| Mouse: Cx3cr1tm2.1(cre/ERT2)Jung |
The Jackson Laboratory | Yona et al., 2013; JAX stock #020940 |
| Mouse: ROSA26iDTR | The Jackson Laboratory | Buch et al., 2005; JAX stock #003173 |
| Recombinant DNA | ||
| Plasmid: pCAG-SIRPα | This paper | N/A |
| Plasmid: pCAG-CD47 | This paper | N/A |
| Plasmid: pCAG-GFP (in pcDNA3.1) | Gift from Elizabeth Zuniga-Sanchez, Matsuda and Cepko, 2007 | N/A |
| Plasmid: pCAG in pcDNA3.1 | Gift from Elizabeth Zuniga-Sanchez | N/A |
| Plasmid: Sirpa mouse tagged ORF clone | ORIGENE | Cat# MG208194 |
| Plasmid: Cd47 mouse tagged ORF clone | ORIGENE | Cat# MG204706 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Diphtheria toxin | Sigma | Cat#D0564 |
| Tamoxifen | Sigma | Cat#T5648 |
| 10X PBS | VWR | Cat#101175-842 |
| Normal Donkey Serum | Jackson ImmunoResearch Labs | Cat#017-000-121 |
| Triton X-100 | EMD | Cat#TX1568-1 |
| Vectashield | Vector Labs | Cat#H-1000-10 |
| FastGreen Dye | Sigma | Cat#F7252-5G |
| RNAscope Probe Mm-Sirpa-C1 | ACD-Biotechne | Cat#837091 |
| RNAscope Probe Mm-Cd47-C2 | ACD-Biotechne | Cat#515461-C2 |
| pHrodo Red Zymosan Bioparticles Conjugate for Phagocytosis | Thermo Fisher | Cat#017-000-121 |
| DMEM/F12 (1:1) | Gibco | Cat#11039-021 |
| B27 (50X) | Gibco | Cat#17504-044 |
| BDNF | Invitrogen | Cat#PHC7074 |
| Dnase I | Sigma | Cat#D4527 |
| Papain | Worthington | Cat#LS003126 |
| MEM | Gibco | Cat#11090 |
| Bovine serum albumin (BSA) | Sigam | Cat#A-9418 |
| Ovomucoid | Worthington | Cat#LS003087 |
| L-cysteine | Sigma | Cat#C1276 |
| 2.5% Phenylephrine Hydrochloride Ophthalmic Solution | Akorn | NDC: 17478-201-15 |
| 1% Tropicamide Ophthalmic Solution | Akorn | NDC: 17478-101-12 |
| Gonak 3ypromellose ophthalmic demulcent solution | Akorn | NDC: 17478-064-12 |
| cOmplete protease inhibitor | Roche | Cat#04693124001 |
| Phosphatase inhibitor I | Calbiochem | Cat#524624 |
| Phosphatase inhibitor II | Calbiochem | Cat#524625 |
| Oligonucleotides | ||
| qRT-PCR primers | ||
| β actin | Fwd – TGAGAGGGAAATCGTGCGTG Rev – TCGTTGCCAATAGTGATGACCTG |
Anderson et al., 2019 |
| Cx3cr1 | Fwd – AAAAACACTGGATTTCAGGGGC Rev – CAACCAACACAGGAACAGGGAG |
Anderson et al., 2019 |
| Mertk | Fwd – CGCTCTGGAGTGGAGGCAC Rev – AAACGCAACAGGAGGTAGGAG |
Anderson et al., 2019 |
| CD68 | Fwd – GGACACTTCGGGCCATGTTT Rev – CTTACACAGTGGACTGGGGC |
Anderson et al., 2019 |
| C1qb | Fwd – ATGGATGCGTAATCACGGGG Rev – GTCTGGGTTTCAGGCAGTCAAG |
Anderson et al., 2019 |
| C3 | Fwd – TCTGACCTCTGGGGAGAAAAGC Rev – TGGGACAACCATAAACCACCATAG |
Anderson et al., 2019 |
| Cd11b | Fwd – TGTGGACTCTCATGCCTCCT Rev – TGGTCATCTCTGAAGCCGTG |
Anderson et al., 2019 |
| VNR | Fwd – CGTCCTCCAGGATGTTTCTCC Rev – GCTTTGACCTCACAGAGGC |
Anderson et al., 2019 |
| Ccr2 | Fwd – GCTGTGTTTGCCTCTCTACCAG Rev – CAAGTAGAGGCAGGATCAGGCT |
NCBI Primer-BLAST |
| Mfge8 | Fwd – GAGCAACAGTGCCAAGGAATGG Rev – ACTGTGGGCTACCTTGTAGGAC |
NCBI Primer-BLAST |
| Tyrobp | Fwd – GGACCCGGAAACAACACATTG Rev – GATCCCAGAGAGGGCTTGTT |
Anderson et al., 2019 |
| LRP | Fwd – GTGTCCAACTGCACAGCAAG Rev – GCAGACGTGAATGTCGCAAT |
Anderson et al., 2019 |
| Softwares | ||
| Imaris, version 9 | Bitplane | http://www.bitplane.com/imaris |
| FIJI | SciJava | https://fiji.sc |
| GraphPad Prism, version 9 | GraphPad Software | http://www.graphpad.com/scientific-software/prism |
| Others | ||
| BTX Harvard Apparatus Tweezertrodes | BTX | Cat#BTX450166 |
| BTX Electroporation System | BTX | Cat#ECM830 |
| Capillary Glass | Sutter Instrument | Cat#BF100-50-10 |
| Fluoview FV1200 confocal microscope | Olympus | Model FV1200 |
| STORM microscope | Bruker | Model Vutara 352 |
| Celeris ERG system | Diagnosys LLC | N/A |
| Kimble Kontes Pellet Pestle homogenizer | DWK Life Sciences | Cat#749540-0000 |
| CFX384 Touch Real-Time PCR Detection System | BioRad | N/A |