Appendix 1—key resources table.
| Reagent type (species) or resource | Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Cell line (Human) | HEK 293T | Sigma | Authenticated with STR profiling, tested negative for mycoplasma | |
| Antibody | Anti-RFP (goat polyclonal) | Rockland | Cat#: 200-101-379 (RRID:AB_2744552) | IF (1:2000) |
| Antibody | Anti-RFP (rabbit polyclonal) | Rockland | Cat#: 600-401-379 (RRID:AB_2209751) | IF (1:2000) |
| Antibody | Anti-PV (mouse monoclonal) | Sigma | Cat#: P3088 (RRID:AB_477329) | IF (1:1000) |
| Antibody | Anti-PV (rabbit polyclonal) | Frontier Institute | Cat#: PV-Rb-Af750 (RRID:AB_2571613) | IF (1 μg/ml) |
| Antibody | Anti-Sst antibody (rabbit polyclonal) | Peninsula Lab | Cat#: T-41003.0050 | IF (1:2000) |
| Antibody | Anti-VIAAT (goat polyclonal) | Frontier Institute | Cat#: PV-Rb-Af750 (RRID:AB_2571613) | IF (1 μg/ml) |
| Antibody | Anti-VIAAT (rabbit polyclonal) | Frontier Institute | Cat#: VGAT-Rb-Af500 (RRID:AB_2571622) | IF (1 μg/ml) |
| Antibody | Anti-NL3 (rabbit polyclonal) | Frontier Institute | Cat#: Nlgn3-Gp-Af880 (RRID:AB_2571814) | IF (1 μg/ml) |
| Antibody | Anti-VGluT3 (goat polyclonal) | Frontier Institute | Cat#: VGluT3-Go-Af870 (RRID:AB_2571854) | IF (1 μg/ml) |
| Antibody | Anti-CB1 (rabbit polyclonal) | Frontier Institute | Cat#: CB1-Rb-Af380 (RRID:AB_2571591) | IF (1 μg/ml) |
| Antibody | Cy3-AffiniPure Donkey anti-Guinea pig IgG | Jackson ImmunoResearch | Cat# 706-165-148 (RRID:AB_2340460) | IF (1:200) |
| Antibody | Donkey anti-Rabbit IgG, Alexa Fluor 488 | Invitrogen | Cat#: A-21206 (RRID:AB_2535792) | IF (1:200) |
| Antibody | Donkey anti-Goat IgG, Alexa Fluor 488 | Invitrogen | Cat#: A-11055 (RRID:AB_2534102) | IF (1:200) |
| Antibody | Donkey anti-Goat IgG, Alexa Fluor 647 | Invitrogen | Cat#: A-21447 (RRID:AB_2535864) | IF (1:200) |
| Antibody | Donkey anti-Rabbit IgG, Alexa Fluor 647 | Invitrogen | Cat#: A-31573 (RRID:AB_2536183) | IF (1:200) |
| Antibody | Anti-Fluorescein-POD, Fab fragments from sheep | Roche | Cat#: 11426346910 (RRID:AB_840257) | FISH (1:500) |
| Antibody | Anti-Digoxigenin-POD, Fab fragments from sheep | Roche | Cat#: 11207733910 (RRID:AB_840257) | FISH (1:500) |
| Chemical compound, drug | tRNA from brewer’s yeast | Roche | Cat#:10109517001 | FISH |
| Chemical compound, drug | Sheep serum | Sigma-Aldrich | Cat#: S3772 | FISH |
| Chemical compound, drug | DAPI | Sigma-Aldrich | Cat#: D9542 | Nuclear staining (1:5000) |
| Chemical compound, drug | Kynurenic acid | Sigma-Aldrich | Cat#: K3375 | Electrophysiology |
| Recombinant DNA reagent | pCAG-HA-Nlgn3Δ (plasmid) | Uchigashima et al., 2020 | Subclone HA- Nlgn3Δ in pCAG vector | |
| Recombinant DNA reagent | pCAG-HA-Nlgn3A2 (plasmid) | Uchigashima et al., 2020 | Subclone HA- Nlgn3A2 in pCAG vector | |
| Recombinant DNA reagent | pCAG-Tag-BFP (plasmid) | This paper | Tag-BFP (Evrogen) | Subclone Tag-BFP in pCAG vector |
| Recombinant DNA reagent | pCAG-EGFP (plasmid) | Futai et al., 2013 | EGFP (Clontech) | Subclone EGFP in pCAG vector |
| Recombinant DNA reagent | pCAG-HA-αNrxn1 + AS4 (plasmid) | This paper | Subclone HA-αNrxn1 + AS4 in pCAG vector | |
| Recombinant DNA reagent | pCAG-HA-αNrxn1 – AS4 (plasmid) | Futai et al., 2013 | Subclone HA-αNrxn1 – AS4 in pCAG vector | |
| Recombinant DNA reagent | pCAG-HA-αNrxn3 + AS4 (plasmid) | This paper | Subclone HA-αNrxn3 + AS4 in pCAG vector | |
| Recombinant DNA reagent | pCAG-HA-αNrxn3 – AS4 (plasmid) | Kang et al., 2008 | Subclone HA-αNrxn3 – AS4 in pCAG vector | |
| Recombinant DNA reagent | pCAG-HA-βNrxn3 + AS4 (plasmid) | This paper | Subclone HA-βNrxn3 + AS4 in pCAG vector | |
| Recombinant DNA reagent | pCAG-HA-βNrxn3 – AS4 (plasmid) | This paper | Subclone HA-βNrxn3 – AS4 in pCAG vector | |
| Recombinant DNA reagent | shNlgn3#1 | Sigma Aldrich | TRCN0000031940 | shRNA in pLKO.1 vector |
| Recombinant DNA reagent | shNlgn3#2 | Sigma Aldrich | TRCN0000031939 | shRNA in pLKO.1 vector |
| Recombinant DNA reagent | pBS SK (-)-αNrxn1#1 (plasmid) | Uchigashima et al., 2019 | Subclone αNrxn1 (186–631, NM_020252.3) in pBS SK (-) vector | |
| Recombinant DNA reagent | pBS SK (-)-αNrxn1#2 (plasmid) | Uchigashima et al., 2019 | Subclone αNrxn1 (631–1132, NM_020252.3) in pBS SK (-) vector | |
| Recombinant DNA reagent | pBS SK (-)-βNrxn1#1 (plasmid) | Uchigashima et al., 2019 | Subclone βNrxn1 (379–824, XM_006523818.2) in pBS SK (-) vector | |
| Recombinant DNA reagent | pBS SK (-)-βNrxn1#2 (plasmid) | Uchigashima et al., 2019 | Subclone βNrxn1 (882–1490, XM_006523818.2) in pBS SK (-) vector | |
| Recombinant DNA reagent | pBS SK (-)-αNrxn2#1 (plasmid) | Uchigashima et al., 2019 | Subclone αNrxn2 (120–370, NM_001205234) in pBS SK (-) vector | |
| Recombinant DNA reagent | pBS SK (-)-αNrxn2#2 (plasmid) | Uchigashima et al., 2019 | Subclone αNrxn2 (894–1209, NM_001205234) in pBS SK (-) vector | |
| Recombinant DNA reagent | pBS SK (-)-βNrxn2#1 (plasmid) |
Uchigashima et al., 2019 | Subclone βNrxn2 (188–375, AK163904.1) in pBS SK (-) vector | |
| Recombinant DNA reagent | pBS SK (-)-βNrxn2#2 (plasmid) |
Uchigashima et al., 2019 | Subclone βNrxn2 (543–714, AK163904.1) in pBS SK (-) vector | |
| Recombinant DNA reagent | pBS SK (-)-αNrxn3#1 (plasmid) |
Uchigashima et al., 2019 | Subclone αNrxn3 (207–795, NM_001198587) in pBS SK (-) vector | |
| Recombinant DNA reagent | pBS SK (-)-αNrxn3#2 (plasmid) |
Uchigashima et al., 2019 | Subclone αNrxn3 (796–1782, NM_001198587) in pBS SK (-) vector | |
| Recombinant DNA reagent | pBS SK (-)-βNrxn3#1 (plasmid) |
Uchigashima et al., 2019 | Subclone βNrxn3 (85–530, NM_001252074) in pBS SK (-) vector | |
| Recombinant DNA reagent | pBS SK (-)-βNrxn3#2 (plasmid) |
Uchigashima et al., 2019 | Subclone βNrxn3 (771–1235, NM_001252074) in pBS SK (-) vector | |
| Recombinant DNA reagent | pBS SK (+)-VGT3 (plasmid) |
Omiya et al., 2015 | Subclone VGluT3 (22–945, NM_182959) in pBS SK (+) vector | |
| Recombinant DNA reagent | pBS SK (+)-Pv (plasmid) |
Yamasaki et al., 2016 | Subclone Parv (57–389, NM_013645) in pBS SK (+) vector | |
| Recombinant DNA reagent | pBS SK (+)-Sst (plasmid) |
Song et al., 2014 | Subclone Sst (133–408, NM_012659) in pBS SK (+) vector | |
| Commercial assay or kit | Fluorescein RNA Labeling Mix | Roche | Cat#: 11685619910 | cRNA probe synthesis kit |
| Commercial assay or kit | DIG RNA Labeling Mix | Roche | Cat#: 11277073910 | cRNA probe synthesis kit |
| Commercial assay or kit | T3 RNA Polymerase | Promega | Cat#: P2083 | cRNA probe synthesis |
| Commercial assay or kit | T7 RNA Polymerase | Promega | Cat#: P2075 | cRNA probe synthesis |
| Commercial assay or kit | Blocking reagent | Roche | Cat#: 11096176001 | FISH |
| Commercial assay or kit | TSA Blocking reagent | PerkinElmer | Cat#: FP1020 | FISH |
| Commercial assay or kit | TSA Plus Cyanine three and Fluorescein System | PerkinElmer | Cat#: NEL753001KT | FISH |
| Commercial assay or kit | SMRT-Seq HT Kit | Takara Bio | Cat# 64437 | RNA-seq library prep kit |
| Commercial assay or kit | Nextera XT DNA Library Preparation Kit | Illumina | FC-131–1096 | RNA-seq library prep kit |
| Commercial assay or kit | Nextera XT Index Kit v2 Set A | Illumina | FC-131–2001 | RNA-seq library prep kit |
| Commercial assay or kit | NovaSeq 6000 S1 Reagent Kit (100 cycles) | Illumina | 20012865 | Illumina sequencing reagent |
| Software, algorithm | BBTools | DOE Joint Genome Institute |
https://jgi.doe.gov/data-and-tools/bbtools/
(RRID:SCR_016968) |
RNA-seq read filtering and trimming |
| Software, algorithm | HISAT2 | Center for Computational Biology at Johns Hopkins University |
https://ccb.jhu.edu/software/hisat2/manual.shtml
(RRID:SCR_015530) |
RNA-seq read alignment |
| Software, algorithm | HTSeq | Simon Anders and Fabio Zanini |
https://htseq.readthedocs.io/en/master/overview.html
(RRID:SCR_005514) |
RNA-seq read quantification |
| Software, algorithm | kallisto | Lior Pachter lab |
https://pachterlab.github.io/kallisto/about
(RRID:SCR_016582) |
RNA-seq pseudoalignment |
| Software, algorithm | R | The R Foundation | https://www.r-project.org/ | Bioinformatic data manipulation, calculation and graphical display |
| Software, algorithm | MetaMorph | Molecular devices |
https://www.moleculardevices.com/?_ga = 2.213249172.1046710400.1598576508–1999962342.1597912565 (RRID:SCR_002368) |
Intensity and count analysis |
| Software, algorithm | ImageJ |
https://imagej.nih.gov/ij/
(RRID:SCR_003070) |
Intensity and count analysis | |
| Software, algorithm | pCLAMP 10.6 | Molecular devices | RRID:SCR_011323 | Electrophysiological data analysis |