| Antibodies |
|
|
|
| Mouse monoclonal anti-ACTC1 (1:50) |
R&D systems |
Cat#: MAB9308-100 |
| Mouse monoclonal anti-ANXA4 (1:200) |
Sigma-Aldrich |
Cat#: SAB4200121; RRID: AB_10621934 |
| Mouse monoclonal anti-ATP1A1 (1:200) |
Novus Biologicals |
Cat#: NB300-146; RRID: AB_2060981 |
| Rabbit polyclonal anti-BSND (1:750) |
Novus Biologicals |
Cat#: NBP2-49101 |
| Mouse monoclonal anti-CDH1 (1:50) |
BD Transduction Laboratories |
Cat#: 610182; RRID: AB_397581 |
| Rabbit polyclonal anti-CDH23 (1:50) |
Invitrogen |
Cat#: PA5-53564; RRID: AB_2639592 |
| Rabbit polyclonal anit-DACH1 (1:50) |
Invitrogen |
Cat#: PA5-52968; RRID: AB_2640365 |
| Mouse monoclonal anti-GATA3 (1:500) |
BD Transduction Laboratories |
Cat#: 558686; RRID: AB_2108590 |
| Rabbit polyclonal anti-GJB2 (1:100) |
Alomone Labs |
Cat#: ACC-212; RRID: AB_11124274 |
| Rabbit polyclonal anti-GJB6 (1:100) |
Invitrogen |
Cat#: PA5-11640; RRID: AB_2111053 |
| Rabbit monoclonal anti-LGR6 (1:100) |
Abcam |
Cat#: ab126747; RRID: AB_11132458 |
| Mouse monoclonal anti-MLANA (1:50) |
Abcam |
Cat#: ab731; RRID: AB_305836 |
| Rabbit polyclonal anti-MYO7A (1:100) |
Proteus Biosciences |
Cat#: 25-6790; RRID: AB_10015251 |
| Rabbit monoclonal anti-MYO7A (1:50) |
Novus Biologicals |
Cat#: NBP1-84266; RRID: AB_11016173 |
| Mouse monoclonal anti-MYO7A (1:30) |
DSHB |
Cat#: 138-1s; RRID: AB_2282417 |
| Mouse monoclonal anti-MYOG (1:10) |
DSHB |
Cat#: F5D; RRID: AB_2146602 |
| Rabbit polyclonal anti-OC90 (1:100) |
Invitrogen |
Cat#: PA5-71564; RRID: AB_2717418 |
| Rabbit polyclonal anti-OCM (1:200) |
Abcam |
Cat#: ab150947 |
| Rabbit polyclonal anti-OTOF (1:100) |
Novus Biologicals |
Cat#: NBP1-46574; RRID: AB_10009850 |
| Rabbit polyclonal anti-OTOR (1:100) |
Invitrogen |
Cat#: PA5-55053; RRID: AB_2645111 |
| Goat polyclonal anti-OTX2 (1:20) |
R&D systems |
Cat#: AF1979; RRID: AB_2157172 |
| Goat polyclonal anti-PDGFRB (1:15) |
R&D systems |
Cat#: AF385; RRID: AB_355339 |
| Mouse monoclonal anti-PECAM1 (1:50) |
Dako |
Cat#: M082329-2 |
| Alexa Fluor™ 568 phalloidin |
Invitrogen |
Cat#: A12380 |
| Chicken polyclonal anti-POU3F4 (1:10000) |
Aves Labs |
Cat#: AB_2814704; RRID: AB_2814704 |
| Rabbit polyclonal anti-SIX1 (1:100) |
Invitrogen |
Cat#: PA5-51654; RRID: AB_2647319 |
| Rabbit polyclonal anti-SLC26A4 (1:100) |
Novus Biologicals |
Cat#: NBP1-85237; RRID: AB_11032075 |
| Mouse monoclonal anti-SOX2 (1:100) |
BD Transduction Laboratories |
Cat#: 561469; RRID: AB_10694256 |
| Goat polyclonal anti-SOX10 (1:50) |
Invitrogen |
Cat#: PA5-47001; RRID: AB_2608449 |
| Rabbit polyclonal anti-TECTA (1:200) |
Invitrogen |
Cat#: PA5-80102; RRID: AB_2747217 |
| Rabbit monoclonal anti-TFAP2A (1:50) |
Abcam |
Cat#: ab108311; RRID: AB_10861200 |
| Rabbit polyclonal anti-TNNT1 (1:500) |
R&D systems |
Cat#: NBP2-38855 |
| Rabbit monoclonal anti-TTR (1:50) |
Invitrogen |
Cat#: MA5-32634; RRID: AB_2809911 |
| Mouse monoclonal anti-TUBB3A (1:100) |
Biolegend |
Cat#: 801202; RRID: AB_10063408 |
| Mouse monoclonal anti-TUBB3A (1:100) |
R&D Systems |
Cat#: MAB1195; RRID: AB_357520 |
| Mouse monoclonal anti-WRHN (1:50) |
Abnova |
Cat#: H00025861-M05; RRID: AB_10629381 |
| Donkey anti-mouse Alexa Fluor™ 488 (1:1000–2000) |
Invitrogen |
Cat#: A21202; RRID: AB_141607 |
| Donkey anti-mouse Alexa Fluor™ 568 (1:1000–2000) |
Invitrogen |
Cat#: A10037; RRID: AB_2534013 |
| Donkey anti-mouse Alexa Fluor™ 594 (1:1000–2000) |
Invitrogen |
Cat#: A21203; RRID: AB_141633 |
| Donkey anti-mouse Alexa Fluor™ 647 (1:1000–2000) |
Invitrogen |
Cat#: A31571; RRID: AB_162542 |
| Donkey anti-mouse Alexa Fluor™ 680 (1:1000–2000) |
Invitrogen |
Cat#: A10038; RRID: AB_2534014 |
| Goat anti-mouse IgG1 Alexa Fluor™ 488 (1:2000) |
Invitrogen |
Cat#: A21121; RRID: AB_2535764 |
| Goat anti-mouse IgG1 Alexa Fluor™ 568 (1:2000) |
Invitrogen |
Cat#: A21124; RRID: AB_2535766 |
| Goat anti-mouse IgG1 Alexa Fluor™ 647 (1:2000) |
Invitrogen |
Cat#: A21240; RRID: AB_2535809 |
| Goat anti-mouse IgG2a Alexa Fluor™ 488 (1:2000) |
Invitrogen |
Cat#: A21131; RRID: AB_2535771 |
| Goat anti-mouse IgG2a Alexa Fluor™ 568 (1:2000) |
Invitrogen |
Cat#: A21134; RRID: AB_2535773 |
| Goat anti-mouse IgG2a Alexa Fluor™ 647 (1:2000) |
Invitrogen |
Cat#: A21241; RRID: AB_2535810 |
| Goat anti-mouse IgG2b Alexa Fluor™ 488 (1:2000) |
Invitrogen |
Cat#: A21141; RRID: AB_2535778 |
| Goat anti-mouse IgG2b Alexa Fluor™ 568 (1:2000) |
Invitrogen |
Cat#: A21144; RRID: AB_2535780 |
| Goat anti-mouse IgG2b Alexa Fluor™ 647 (1:2000) |
Invitrogen |
Cat#: A21242; RRID: AB_2535811 |
| Donkey anti-rabbit Alexa Fluor™ 488 (1:1000) |
Abcam |
Cat#: ab150061; RRID: AB_2571722 |
| Donkey anti-rabbit Alexa Fluor™ 488 (1:1000–2000) |
Invitrogen |
Cat#: A21206; RRID: AB_2535792 |
| Donkey anti-rabbit Alexa Fluor™ 568 (1:1000–2000) |
Invitrogen |
Cat#: A10042; RRID: AB_2534017 |
| Donkey anti-rabbit Alexa Fluor™ 594 (1:1000–2000) |
Invitrogen |
Cat#: A21207; RRID: AB_141637 |
| Donkey anti-rabbit Alexa Fluor™ 647 (1:1000–2000) |
Invitrogen |
Cat#: A31573; RRID: AB_2536183 |
| Donkey anti-rabbit Alexa Fluor™ 680 (1:1000–2000) |
Invitrogen |
Cat#: A10043; RRID: AB_2534018 |
| Donkey anti-goat Alexa Fluor™ 488 (1:1000) |
Abcam |
Cat#: ab150133; RRID: AB_2832252 |
| Goat anti-chicken Alexa Fluor™ 594 (1:1000) |
Invitrogen |
Cat#: A11042; RRID: AB_2534099 |
|
| Chemicals, peptides, and recombinant proteins |
|
|
|
| Stempro Accutase Cell Dissociation Reagent |
Gibco |
Cat#: A1110501 |
| Y27632 |
Stemgent |
Cat#: 04-0012-02 |
| Essential 8 Flex medium |
Gibco |
Cat#: A2858501 |
| Vitronectin |
Gibco |
Cat#: A14700 |
| Normocin |
Invivogen |
Cat#: ant-nr-1 |
| EDTA |
Gibco |
Cat#: 15575020 |
| E6 medium |
Gibco |
Cat#: A1516401 |
| Matrigel Growth Factor Reduced |
Corning |
Cat#: 354230 |
| SB431542 |
Stemgent |
Cat#: 04-0010-05 |
| basic FGF |
Peprotech |
Cat#: 100-18B |
| BMP-4 |
Peprotech |
Cat#: 120-05 |
| BMP-4 |
Stemgent |
Cat#: 03-0007 |
| BMP-4 |
R&D |
Cat#: 314-BP |
| BMP-4 |
R&D |
Cat#: 314-BPE |
| LDN |
Stemgent |
Cat#: 04-0074-02 |
| CHIR99021 |
Stemgent |
Cat#: 04-0004-02 |
| Advanced DMEM:F12 medium |
Gibco |
Cat#: 12634010 |
| Neurobasal medium |
Gibco |
Cat#: 21103049 |
| B27 Supplement without vitamin A |
Gibco |
Cat#: 12587010 |
| N2 Supplement |
Gibco |
Cat#: 17502048 |
| Glutamax |
Gibco |
Cat#: 35050061 |
| β-Mercaptoethanol |
Gibco |
Cat#: 21985023 |
| Low Melting Point Agarose |
Invitrogen |
Cat#: 16520050 |
| PBS |
Gibco |
Cat#: 14190144 |
| TrypLE |
Gibco |
Cat#: 12605036 |
| Bovine Serum Albumin |
Sigma-Aldrich |
Cat#: A7030 |
| Trypan Blue |
Gibco |
Cat#: 15250061 |
| Tris-HCl |
Millipore-Sigma |
Cat#: T2194 |
| NaCl |
Millipore-Sigma |
Cat#: 59222C |
| MgCl2 |
Millipore-Sigma |
Cat#: M1028 |
| Nonidet P40 Substitute |
Millipore-Sigma |
Cat#: 74385 |
| DEPC-treated water |
Invitrogen |
Cat#: 750024 |
| Rnase inhibitor |
Millipore-Sigma |
Cat#: 3335402001 |
| RNAlater |
Invitrogen |
Cat#: AM7020 |
|
| Critical commercial assays |
|
|
|
| Chromium Next GEM Single Cell 3' |
10X Genomics |
Cat#: PN-1000128 |
| Library & Gel Bead Kit v3.1 |
|
|
| Chromium Next GEM Single Cell 3' |
10X Genomics |
Cat#: PN-120267 |
| Library & Gel Bead Kit v2 |
|
|
| Anti-Nuclear Pore Complex Proteins |
Merck |
Cat#: MAb414 |
| Fc-blocking reagent |
Biolegend |
Cat#: 422302 |
|
| Deposited data |
|
|
|
| RNA sequencing data IEO |
This manuscript |
GEO: GSE214099
|
| RNA sequencing data human inner ear |
This manuscript |
GEO: GSE213796
|
|
| Experimental models: Cell lines |
|
|
|
| WA01 ESC line |
WiCell |
N/A |
| AICS-0074 iPSC line (WTC-SOX2) |
Allen Institute |
N/A |
| WTC-GCaMP iPSC line |
Bruce Conklin at the Gladstone Institutes/UCSF |
N/A |
| LUMC0004iCtrl10 iPSC line (LUMC04i10) |
LUMC iPSC Hotel |
N/A |
| LUMC044iCtrl44 iPSC line (LUMC44i44) |
LUMC iPSC Hotel |
N/A |
| SAH0047-02 iPSC line |
BCH Human Neuron Core |
N/A |
| GON0515-03 iPSC line |
BCH Human Neuron Core |
N/A |
| GON0926-02 iPSC line |
BCH Human Neuron Core |
N/A |
|
| Software and algorithms |
|
|
|
| CellChat 1.4.0 |
Jin et al.74
|
https://github.com/sqjin/CellChat
|
| CellRanger 6.1.0 |
10× Genomics |
https://www.10xgenomics.com/support
|
| Rstudio version 1.4.1106 |
Rstudio |
https://www.rstudio.com/
|
| Seurat version 4.1.0 |
Satija et al.118
|
https://satijalab.org/seurat/
|
| ggplot2 version 3.3.6 |
Wickham119
|
https://ggplot2.tidyverse.org/
|
| Nebulosa version 1.0.2 |
Alquicira-Hernandez et al.120
|
www.github.com/powellgenomicslab/Nebulosa
|
| Symphony version 0.1.0 |
Kang et al.65
|
https://github.com/immunogenomics/symphony
|
| ImageJ-Fiji |
ImageJ |
https://imagej.net/software/fiji/
|
| R version 4.0.5 |
R-project |
https://www.r-project.org/
|
| SCTransform version 0.3.3 |
Hafemeister et al.121
|
https://github.com/satijalab/sctransform
|
| LAS X Life Science |
Leica |
https://www.leica-microsystems.com/
|
| Adobe Illustrator 2022 |
Adobe |
https://www.adobe.com/
|
| Adoble Photoshop 2022 |
Adobe |
https://www.adobe.com/
|
| Leica Application Suite (LAS) |
Leica |
https://www.leica-microsystems.com/
|
| SerialEM version 4.0 |
Mastronarde122
|
https://bio3d.colorado.edu/SerialEM/
|
| IMOD version 4.11 |
Kremer et al.123
|
https://bio3d.colorado.edu/imod/
|
|
| Other |
|
|
|
| 96-well U-bottom plates with a super-low cell attachment surface |
Thermo Scientific |
Cat#: 174925 |
| 24-well plates with a super-low cell attachment surface |
Thermo Scientific |
Cat#: 174930 |
| Dounce tissue grinder |
Kimble |
Cat#: 885300-0002 |
| 70 μm MACS SmartStrainer |
Miltenyi Biotec |
Cat#: 130-098-462 |
| 40 μm Flowmi cell strainer |
Bel-Art |
Cat#: H13680-0040 |
| 10 μm Pluristrainer |
PluriSelect |
Cat#: 43-10020-40 |
| 20 μm Pluristrainer |
PluriSelect |
Cat#: 43-10010-40 |
| Cryomolds |
Andwin Scientific |
Cat#: 25608 |
| Ultra 45° diamond knife |
Diatome |
Cat#: Ultra 45° |
| Histo diamond knife |
Diatome |
Cat#: Histo |
| Single-slot copper grids |
Veco |
Cat#: 12563-CU |
| Aminoalkylsilane-coated glass slides |
VWR |
Cat#: 631-1165 |
