KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Rat anti-Ctip2 | Abcam | RRID: AB_2064130 |
| Mouse anti-Cre | Milipore | RRID: AB_2085748 |
| Goat anti-rat | Jackson ImmunoResearch | RRID: AB_2338308 |
| Goat anti-mouse | ThermoFisher | RRID: AB_2534062 |
| AMCA Avidin D antibody | Vector Laboratories | RRID: AB_2336102 |
| Bacterial and virus strains | ||
| pAAV-CAG-hChR2(H134R)-mCherry | Unpublished data | pAAV.CAG.hChR2(H134R)-mCherry.WPRE.SV40 was a gift from Karl Deisseroth (Addgene viral prep # 100054-AAV1; http://addgene.org/100054; RRID: Addgene_100054) |
| pAAV-CAG-flex-ChR2-tdTomato | (Tang et al., 2016) | pAAV-CAG-FLEXFRT-ChR2(H134R)-mCherry was a gift from Connie Cepko (Addgene viral prep # 75470-AAV1; http://addgene.org/75470; RRID: Addgene_75470) |
| AAV-flex-Arch-GFP | (Chow et al., 2010) | AAV-FLEX-Arch-GFP was a gift from Edward Boyden (Addgene viral prep # 22222-AAV1;http://addgene.org/22222; RRID: Addgene_22222) |
| pACAGW-ChR2-Venus-AAV | (Petreanu et al., 2009) | pACAGW-ChR2-Venus-AAV was a gift from Karel Svoboda (Addgene viral prep # 20071-AAV1;http://addgene.org/20071; RRID: Addgene_20071) |
| pAAV-Ef1a-mCherry-IRES-Cre | (Fenno et al., 2014) | pAAV-Ef1a-mCherry-IRES-Cre was a gift from Karl Deisseroth (Addgene viral prep # 55632-AAVrg;http://addgene.org/55632; RRID: Addgene_55632) |
| pAAV-CAG-GFP | Unpublished data | pAAV-CAG-GFP was a gift from Edward Boyden (Addgene viral prep # 37825-AAVrg;http://addgene.org/37825; RRID: Addgene_37825) |
| pAAV-hSyn-mcherry | Unpublished data | pAAV-hSyn-mCherry was a gift from Karl Deisseroth (Addgene viral prep # 114472-AAVrg;http://addgene.org/114472; RRID: Addgene_114472) |
| pAAV-CAG-hChR2(H134R)-mCherry | (Mao et al., 2011) | AAV-CAG-hChR2-H134R-tdTomato was a gift from Karel Svoboda (Addgene viral prep # 28017-AAVrg; http://addgene.org/28017; RRID: Addgene_28017) |
| pENN-AAV-hSyn-Cre | Unpublished data | pENN.AAV.hSyn.Cre.WPRE.hGH was a gift from James M. Wilson (Addgene viral prep # 105553-AAV1; http://addgene.org/105553; RRID: Addgene_105553) |
| AAV-SYN-flex-PSAM4-GlyR-EGFP | (Magnus et al., 2019) | AAV SYN flex PSAM4 GlyR IRES EGFP was a gift from Scott Sternson (Addgene viral prep # 119741-AAV5; http://addgene.org/119741; RRID: Addgene_119741) |
| Chemicals, peptides, and recombinant proteins | ||
| Fluoro-gold | Fluorochorme | Patent No. 4716905 |
| VectaShield without DAPI | Vector Laboratories | RRID: AB_2336789 |
| VectaShield with DAPI | Vector Laboratories | RRID: AB_2336790 |
| Neurobiotin Tracer | Vector Laboratories | Catalog No. SP-1120 |
| Experimental models: Organisms/strains | ||
| Mouse/C57BL/6J | Jackson Lab | RRID: IMSR_JAX:000664 |
| Mouse/CamKII-Cre | Jackson Lab | RRID: IMSR_JAX:005359 |
| Software and algorithms | ||
| MATLAB | MathWorks | https://www.mathworks.com/products/matlab.html?s_tid=hp_products_matlab |
| iPython and Jupyter | (Perez and Granger, 2007) | https://jupyter.org |
| Minitab Statistical Softeware | Minitab | https://www.minitab.com/en-us/products/minitab/ |
| Fiji (ImageJ) | NIH | https://fiji.sc |
| Clustering code | This paper | https://github.com/wyomingneuron/Clustering |