Key resources table.
| Reagent type (species) or resource | Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Cell line (human) | RUES2 | Human embryonic stem cell line | NIH registration number: NIHhESC-09-0013 | |
| Cell line (human) | H9 (WA09) | Human embryonic stem cell line | NIH registration number: NIHhESC-10-0062 | |
| Cell line (human) | ATOH1-EGFP | Human embryonic stem cell line | This study (RUES2 line) |
|
| Cell line (human) | ATOH1-EGFP-L10a | Human embryonic stem cell line | This study (RUES2) | |
| Recombinant DNA reagent | pPS-EF1α-GFP-RFP | System Biosciences | LV603PA-1 | Lentiviral vector |
| Recombinant DNA reagent | J2XnGFP | Dr. Jane Johnson | GFP plasmid | |
| Recombinant DNA reagent | pSIN-hATOH1 enhancer- hβ-globin-nlsEGFP-bGH polyA-hPGK-Puromycin | This study | ATOH1-EGFP lentiviral construct |
|
| Recombinant DNA reagent | pSIN-hATOH1 enhancer- hβ-globin-nlsEGFP-bGH polyA-hPGK-Puromycin | This study | ATOH1-EGFP- L10a lentiviral construct |
|
| Biological sample (human) | Human fetal cerebellum (17 PCW) | Human Developmental Biology Resource | http://www.hdbr.org/ | |
| Biological sample (mouse) | C57Bl/6J mice | Jackson Laboratory | Embryos and pups obtained from times matings |
|
| Antibody | Calretinin (rabbit polyclonal) | Swant | 7699/4 | (1:1000) |
| Antibody | EN2 (C19) (goat polyclonal) | Santa Cruz | SC-8111 | (1:50) |
| Antibody | GFAP (chicken polyclonal) | EnCor | CPCA-GFAP | (1:1500) |
| Antibody | GFP (rabbit polyclonal) | Invitrogen | A-111122 | (1:500) |
| Antibody | GFP (chicken polyclonal) | Aves labs | GFP-1020 | (1:1000) |
| Antibody | HuNu (anti-human nuclei) (mouse monoclonal) | Millipore | MAB1281 | (1:100) |
| Antibody | Ki67 (rabbit monoclonal) | Vector Laboratories | VP-RM04 | (1:100) |
| Antibody | Ki67 (rabbit polyclonal) | EnCor | RPCA-Ki67 | (1:1000) |
| Antibody | Map2 (chicken polyclonal) | Abcam | ab5392 | (1:1000) |
| Antibody | NeuN (mouse monoclonal) | Millipore | MAB377 | (1:100) |
| Antibody | NeuroD1 (mouse monoclonal) | BD Pharmingen | 563000 | (1:300) |
| Antibody | Pax6 (rabbit polyclonal) | BioLegend | 901301 | (1:300) |
| Antibody | TAG1 (mouse monoclonal) | Tom Jessell | (1:2) | |
| Antibody | Synaptophysin (mouse monoclonal) | Millipore | MAB329 | (1:500) |
| Antibody | VGLuT1 (mouse monoclonal) | Millipore | MAB5502 | (1:100) |
| Antibody | SOX2 (rabbit monoclonal) | Cell Signaling | 3579 | (1:200) |
| Antibody | GluR-d2 (goat polyclonal) | Santa Cruz | Sc-26118 | (1:100) |
| Antibody | Anti-goat Alexa Fluor 633 (donkey polyclonal) | Invitrogen | A21082 | (1:300) |
| Antibody | Anti-rabbit Alexa Fluor 555 (donkey polyclonal) | Invitrogen | A-31572 | (1:300) |
| Antibody | Anti-mouse IgM Alexa Fluor 488 (goat polyclonal) | Invitrogen | A-21042 | (1:300) |
| Antibody | Anti-mouse Alexa Fluor 555 (donkey polyclonal) | Invitrogen | A-31570 | (1:300) |
| Antibody | Anti-chicken IgY 488 (donkey polyclonal) | Jackson ImmunoResearch | 703-545-155 | (1:300) |
| Antibody | Anti-chicken IgY Cy3 (donkey polyclonal) | Jackson ImmunoResearch | 703-165-155 | (1:300) |
| Antibody | Anti-rabbit Alexa Fluor 647 (donkey polyclonal) | Invitrogen | A-31573 | (1:300) |
| Antibody | Anti-mouse Alexa Fluor 647 (donkey polyclonal) | Invitrogen | A-31571 | (1:300) |
| Antibody | Anti-mouse Alexa Fluor 488 (donkey polyclonal) | Invitrogen | A-21202 | (1:300) |
| Antibody | Anti-mouse Fluor 405 (donkey polyclonal) | Abcam | Ab175658 | (1:300) |
| Sequence-based reagent | ATOH1 | This paper | PCR primer | Forward 5′-GCGCA AAAGAATTT GTCTCC-3′ |
| Sequence-based reagent | ATOH1 | This paper | PCR primer | Reverse 5′-GCG AAGTTTTGCTG TTTTCC-3′ |
| Sequence-based reagent | ID4 | This paper | PCR primer | Forward 5′-GC TCACTGCGCT CAACACC-3′ |
| Sequence-based reagent | ID4 | This paper | PCR primer | Reverse 5′-GAA TGCTGTCGCC CTGCTTG-3′ |
| Sequence-based reagent | EN2 | This paper | PCR primer | Forward 5′- GG CGTGGGTCTA CTGTACG-3′ |
| Sequence-based reagent | EN2 | This paper | PCR primer | Reverse 5′- TACCTGTTG GTCTGGAA CTCG-3′ |
| Sequence-based reagent | PAX6 | This paper | PCR primer | Forward 5′-TCA CCATGGCAA ATAACCTG-3′ |
| Sequence-based reagent | PAX6 | This paper | PCR primer | Reverse 5′-CA GCATGCAGG AGTATGAGG-3′ |
| Sequence-based reagent | NEUROD1 | This paper | PCR primer | Forward 5′-GGACGA GGAGCAC GAGGCAG ACAAGAA-3′ |
| Sequence-based reagent | NEUROD1 | This paper | PCR primer | Reverse 5′- TTCCTCA GTGAGTCC TCCTCTG CGTTCA-3′ |
| Sequence-based reagent | PCP2 | This paper | PCR primer | Forward 5′- GACC AGGAGGG CTTCTTCAATCT-3′ |
| Sequence-based reagent | PCP2 | This paper | PCR primer | Reverse 5′- CATG TCCATGA GGCTGT CCATCT-3′ |
| Sequence-based reagent | OTX2 | This paper | PCR primer | Forward 5′-ACAA GTGGC CAATTCA CTCC-3′ |
| Sequence-based reagent | OTX2 | This paper | PCR primer | Reverse 5′-GAGG TGGACAA GGGATCTGA-3′ |
| Sequence-based reagent | MEIS2 | This paper | PCR primer | Forward 5′-CCAG GGGACT ACGTTTCTCA-3′ |
| Sequence-based reagent | MEIS2 | This paper | PCR primer | Reverse 5′-TAA CATTGT GGGGC TCTGTG-3′ |
| Sequence-based reagent | GBX2 | This paper | PCR primer | Forward 5′-GTTCC CGCCG TCGCTGATGAT-3′ |
| Sequence-based reagent | GBX2 | This paper | PCR primer | Reverse 5′-GCC GGTGTA GACGAA ATGGCCG-3′ |
| Sequence-based reagent | HOXA2 | This paper | PCR primer | Forward 5-CGT CGCTC GCTGA GTGCCTG-3′ |
| Sequence-based reagent | HOXA2 | This paper | PCR primer | Reverse 5′-TGTC GAGTGTG AAAGCG TCGAGG-3′ |
| Sequence-based reagent | LHX2 | This paper | PCR primer | Forward 5′- GGTCCTC CAGGTCT GGTTC-3′ |
| Sequence-based reagent | LHX2 | This paper | PCR primer | Reverse 5′- TAAGAG GTTGCGC CTGAACT-3′ |
| Sequence-based reagent | LHX9 | This paper | PCR primer | Forward 5′- GCT GGGAGT GGACATCGTCA-3′ |
| Sequence-based reagent | LHX9 | This paper | PCR primer | Reverse 5′- CATG GTCCGGA GCTGGTGAT-3′ |
| Sequence-based reagent | β-ACTIN | This paper | PCR primer | Forward 5′-AAAC TGGAAC GGTGAAGG-3′ |
| Sequence-based reagent | β-ACTIN | This paper | PCR primer | Reverse 5′-AGA GAAGT GGGGTGGCTT-3′ |
| Sequence-based reagent | ATP5O | This paper | PCR primer | Forward 5′- cgcta tgccac agctcttta-3′ |
| Sequence-based reagent | ATP5O | This paper | PCR primer | Reverse 5′- atgg aacgcttc acataggg-3′ |
| Peptide, recombinant protein | Human bFGF | Invitrogen | Catalog # 13256-029 | |
| Peptide, recombinant protein | Human/mouse/ ratBDNF |
PeproTech | Catalog # 450-02 | |
| Peptide, recombinant protein | Mouse BMP7 | R&D Systems | Catalog # 5666BP-010 | |
| Peptide, recombinant protein | Human recombinant insulin | Tocris | Catalog # 3435 | |
| Peptide, recombinant protein | Human BMP4 | R&D Systems | Catalog # 314BP-050 | |
| Peptide, recombinant protein | Human BMP6 | R&D Systems | Catalog # 507BP-020 | |
| Peptide, recombinant protein | Human/mouse FGF8b | R&D Systems | Catalog # 423-F8-025 | |
| Commercial assay or kit | RNeasy micro kit | QIAGEN | Catalog # 74004 | |
| Commercial assay or kit | RNeasy Plus mini kit | QIAGEN | Catalog # 74134 | |
| Commercial assay or kit | Transcription First Strand cDNA Synthesis Kit | Roche Life Sciences | Catalog # 04379012001 | |
| Commercial assay or kit | HotStarTaq PLUS DNA Polymerase kit | QIAGEN | Catalog # 203603 | |
| Commercial assay or kit | Click-iT EdU Cell Proliferation Kit for Imaging | Invitrogen | Catalog # C10338 | |
| Commercial assay or kit | SMART-Seq v4 Ultra Low Input RNA Kit | TaKaRa Bio | Catalog # 634888 | |
| Commercial assay or kit | Nextera XT DNA library preparation kit | Illumina | Catalog # FC-131-1024 | |
| Commercial assay or kit | RNA 6000 Pico Kit | Agilent | Catalog # 5067-1513 | |
| Commercial assay or kit | In-fusion HD cloning plus (Clontech) | TaKaRa Bio | Catalog # 638909 | |
| Commercial assay or kit | Anti-mouse IgM microbeads | Miltenyi Biotec | Catalog # 130-047-302 | |
| Commercial assay or kit | MS columns | Miltenyi Biotec | Catalog # 130-042-201 | |
| Chemical compound, drug | ROCK-inhibitor Y-27632 | Abcam | Catalog # ab 120129 | |
| Chemical compound, drug | SB431542 | Tocris | Catalog # 1614 | |
| Chemical compound, drug | LDN-193189 | Stemgent/ Tocris |
Catalog # 6053 | |
| Chemical compound, drug | CHIR99021 | Stemgent/ REPROCELL |
Catalog # 04-0004-02 | |
| Software, algorithm | Primer3 | Open source | Primer3, RRID:SCR_003139 | |
| Software, algorithm | Salmon quantification software (version 0.8.2) | Open source |
|
Salmon, RRID:SCR_017036 (Patro et al., 2017) |
| Software, algorithm | R statistical software | Open source | R Project for Statistical Computing, RRID:SCR_001905 | |
| Software, algorithm | Tximport (version 1.8.0). | Open source | tximport, RRID:SCR_016752 (Love et al., 2016) |
|
| Software, algorithm | DESeq2 (version 1.20.0) | Open source | DESeq2, RRID:SCR_015687 (Love et al., 2018) |
|
| Software, algoritham Software, algorithm |
rtracklayer package (version 1.40.6) | Open source | rtracklayer, RRID:SCR_021325 | |
| Software, algorithm | GSVA (version 1.34.0) | Open source(Hänzelmann et al., 2013) | GSVA, RRID:SCR_021058 | |
| Software, algorithm | Pheatmap R package (version 1.0.10) | Open source | ncv | pheatmap, RRID:SCR_016418 |
| Software, algorithm | topGO Bioconductor package | Open source | topGO, RRID:SCR_014798 | |
| Software, algorithm | GOseq Bioconductor package | Open source (Young et al., 2010) | Goseq, RRID:SCR_017052 | |
| Software, algorithm | ImageJ (version 2.1.0/1.53c) | Open source, NIH | ImageJ, RRID:SCR_003070 | |
| Software, algorithm | SPSS software | IBM | ||
| Software, algorithm | BD FACSDiva 8.0.1 software |
BD Biosciences | ||
| Software, algorithm | ZEN imaging software | Zeiss |