KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
|
| ||
| Antibodies | ||
|
| ||
| Rabbit polyclonal anti-myosin-7a | Proteus Biosciences | #25–6790; RRID:AB_10015251 |
| Mouse monoclonal anti-Sox2 | Santa Cruz Biotechnology | #sc-365823; RRID:AB_10842165 |
| Rabbit polyclonal anti-neurofilament 200 | Sigma | #N4142; RRID:AB_477272 |
| Donkey anti-rabbit IgG, Alexa Fluor 546 | Thermo Fisher Scientific | # 2534016; RRID:AB_2534016 |
| Donkey anti-mouse IgG, Alexa Fluor 488 | Thermo Fisher Scientific | #141607; RRID:AB_141607 |
|
| ||
| Chemicals, peptides, and recombinant proteins | ||
|
| ||
| Alexa Fluor 647 Phalloidin | Invitrogen | # 2620155 |
| Paraformaldehyde | EMS | #15710 |
| DAPI | Thermo Fisher Scientific | #2629482 |
| Mounting Media (Citifluor CFM-3) | EMS | #17979–30 |
| Recombinant human FGF | Peprotech | #100–18 |
| Recombinant human IGF-1 | R&D | #291-G1–200 |
| Laminin from human placenta | Sigma | #L6274 |
| ACCUTASE | Innovative Cell Technology | #AT 104 |
| DMEM-F12 basal medium | Gibco | #11320033 |
| N2 | ThermoFisher Scientific | #17502048 |
| Phospho-vitamin C | Sigma | #49752 |
| Matrigel | Corning | #356234 |
| Trypsin-EDTA | GIBCO | #25200–056 |
| Phosphate-buffered saline | GIBCO | #10010 |
| Polybrene Infection/Transfection Reagent | Sigma | #TR-1003-G |
| Human Wnt3a | R&D | #5036-GMP-010 |
| Antibiotics (Penicillin-Streptomycin) | Gibco | #15–140-163 |
| Antifungal (Amphotericin B) | Gibco | #15290018 |
| BIX01294 | Sigma | #B9311 |
| CHIR99021 | LC Labs | #C-6556 |
| LY411575 | Sigma | #SML0506 |
| VPA | Sigma | #P4543 |
|
| ||
| Critical commercial assays | ||
|
| ||
| Chromium Single Cell 50 Library | 10x Genomics | #PN-1000006 |
| Chromium Next GEM Single Cell | 10x Genomics | #PN-1000263 |
|
| ||
| Deposited data | ||
|
| ||
| Organoids D0, D2, D4, D10 | This paper | GSE132635 |
| Inner hair cells P1, P7 | This paper | GSE137299 |
| Outer hair cells P1, P7 | This paper | GSE137299 |
| Type I HCs P7, P12, P100 | This paper | GSE115934 |
| Type II HCs P7, P12, P100 | This paper | GSE115934, GSE172327 |
| Type 1 SGNs P63, P25–27 | This paper | GSE114759, GSE114997 |
| Type 2 SGNs P63, P25–27 | This paper | GSE114759, GSE114997 |
| Hensen’s E16, P1 | This paper | GSE137299 |
| Inner pillar E16, P1, P2, P7 | This paper | GSE137299, GSE172327 |
| Outer pillar P1, P2, P7 | This paper | GSE137299 |
| Inner phalangeal E16, P1, P2, P7 | This paper | GSE137299 |
| Claudius E16, P1 | This paper | GSE137299 |
| Deiters’ row 1,2 P1, P2, P7 | This paper | GSE137299 |
| Deiters’ row 3 P1, P2, P7 | This paper | GSE137299 |
| Utricular SCs P1, P2 | This paper | GSE71982, GSE172327 |
| Marginal P30 | This paper | GSE136196 |
| Intermediate P30 | This paper | GSE136196 |
| Basal P30 | This paper | GSE136196 |
|
| ||
| Software and algorithms | ||
|
| ||
| ImageJ | Fiji | http://fiji.sc/ |
| Prism Version 8.4.1 | GraphPad | https://www.graphpad.com/features |
| Cell Ranger Version 2.1.0 | 10x Genomics | https://support.10xgenomics.com/single-cell-gene-expression/software/downloads |
| ProjectR R Package | Yu et al.34 | https://www.bioconductor.org/packages/release/bioc/html/projectR.html |
| MACS version 2.1 | Zhang et al.35 | https://pypi.org/project/MACS2/ |
| DiffBind | Ross-Innes et al.36 | https://bioconductor.org/packages/release/bioc/html/DiffBind.html |
| HOMER | Heinz et al.13 | http://homer.ucsd.edu/homer/motif/ |
| Seurat v3 Standard Workflow | Butler et al.37 | https://satijalab.org/seurat/ |
| Monocle Version 2.14.0 | Trapnell et al.38 | http://cole-trapnelllab.github.io/monocle-release/monocle3/ |
| GENIE3 | Huynh-Thu et al.11 | https://bioconductor.org/packages/release/bioc/html/GENIE3.html |