KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
|
| ||
| Rabbit-anti-H3K4me3 | Active motif | Cat#39159; Lot#01609004; RRID: AB_2615077 |
| Rabbit-anti-H3K4me1 | Active motif | Cat#61633; Lot#31814001; RRID: AB_2793712 |
| Rabbit-anti-H3K27ac | Active motif | Cat#39133; Lot#:01518010; RRID: AB_2561016 |
| Rabbit-anti-H3K27me3 | Active motif | Cat#39155; Lot#31618020; RRID: AB_2561020 |
| Rabbit-anti-mouse | Abcam | Cat#ab46540; RRID: AB_2614925 |
| Rabbit-anti-GFP | Torrey Pines Biolabs | Cat#TP401; Lot#071519; RRID: AB_10013661 |
| Rabbit-anti-MYO6 | Proteus Biosciences | Cat#25-6791; RRID: AB_2314836 |
| Mouse-anti-POU4F3 | Santa Cruz | Cat#sc-81980; RRID: AB_2167543 |
| Goat-anti-mouse-Alex-647 | Thermo Fisher | Cat#A-21235; RRID: AB_2535804 |
| Goat-anti-rabbit-Alex-647 | Thermo Fisher | Cat#A-21245; RRID: AB_2535813 |
|
| ||
| Chemicals, Peptides, and Recombinant Proteins | ||
|
| ||
| DAPT | Calbiochem | Cat#565770; CAS# 208255-80-5 |
| GSK-343 | GSK | CAS#1346704-33-3 |
| TSA | Sigma | Cat#T1952; CAS# 58880-19-6 |
| GSK-LSD1 | Sigma | Cat#SML1072; CAS# 1431368-48-7 |
| (Z)-4-Hydroxytamoxifen | Sigma | Cat#H7904; CAS# 68047-06-3 |
| pA-Mnase | Skene and Henikoff, 2017 | N/A |
|
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| Critical Commercial Assays | ||
|
| ||
| Quick RNA-microprep kit | Zymo | Cat#R1051 |
| QIAseq FX Single Cell RNA Library Kit | Qiagen | Cat# 180735 |
| Accel-NGS 2S plus DNA prep kits | Swift Biosciences | Cat#21096 |
| 2S Set A+B MID Indexing Kit | Swift Biosciences | Cat#27396 |
|
| ||
| Deposited Data | ||
|
| ||
| P1HC_RNAseq | this paper | GSE150000 |
| P1SC_RNAseq | this paper | GSE150000 |
| P1SC_TSA_48h_RNAseq | this paper | GSE150001 |
| P1SC_GSK343_48h_RNAseq | this paper | GSE150001 |
| P1SC_DMSO_48h_RNAseq | this paper | GSE150001 |
| P1SC_DAPT_24h_RNAseq | this paper | GSE150002 |
| P1SC_DMSO_24h_RNAseq | this paper | GSE150002 |
| P1SC_control_48h_RNAseq | this paper | GSE150002 |
| P1SC_nonresponsive_48h_RNAseq | this paper | GSE150002 |
| P1SC_responsive_48h_RNAseq | this paper | GSE150002 |
| P1HC_ATACseq | this paper | GSE150000 |
| P1HC_H3K4me1_CUT&RUN | this paper | GSE150000 |
| P1HC_H3K4me3_ChIPseq | this paper | GSE150000 |
| P1HC_H3K27ac_ChIPseq | this paper | GSE150000 |
| P1HC_H3K27me3_ChIPseq | this paper | GSE150000 |
| P1HC_ATOH1_CUT&RUN | this paper | GSE150000 |
| P1SC_ATACseq | this paper | GSE150000 |
| P1SC_H3K4me3_CUT&RUN | this paper | GSE150000 |
| P1SC_H3K4me1_CUT&RUN | this paper | GSE150000 |
| P1SC_H3K27ac_CUT&RUN | this paper | GSE150000 |
| P1SC_H3K27me3_ChIPseq | this paper | GSE150000 |
| P1SC_control_48h_ATACseq | this paper | GSE150002 |
| P1SC_control_48h_H3K27ac_CUT&RUN | this paper | GSE150002 |
| P1SC_nonresponsive_48h_ATACseq | this paper | GSE150002 |
| P1SC_nonresponsive_48h_H3K27ac_CUT&RUN | this paper | GSE150002 |
| P1SC_responsive_48h_ATACseq | this paper | GSE150002 |
| P1SC_responsive_48h_H3K27ac_CUT&RUN | this paper | GSE150002 |
| E17SC_H3K4me3_ChIPseq | this paper | GSE150000 |
| E17SC_H3K4me1_CUT&RUN | this paper | GSE150000 |
| P6SC_H3K4me3_CUT&RUN | this paper | GSE150000 |
| P6SC_H3K4me1_CUT&RUN | this paper | GSE150000 |
| P1SC_Base_H3K4me1_CUT&RUN | this paper | GSE150000 |
| P1SC_Apex_H3K4me1_CUT&RUN | this paper | GSE150000 |
| P21cSC_ATACseq | this paper | GSE150000 |
| P21cSC_H3K4me1_CUT&RUN | this paper | GSE150000 |
| P21uSC_ATACseq | this paper | GSE150000 |
| P21uSC_H3K4me1_CUT&RUN | this paper | GSE150000 |
|
| ||
| Experimental Models: Cell Lines | ||
|
| ||
| 293T cells | ATCC | ATCC®CRL-3216™ |
|
| ||
| Experimental Models: Organisms/Strains | ||
|
| ||
| Mouse: Atoh1-Gfp: B6.129S-Atoh1tm4.1Hzo/J | Jackson Laboratory | JAX: 013593 |
| Mouse: Lfng-Gfp: Tg(Lfng-EGFP)HM340Gsat | Gong et al., 2003 | MGI:4847192 |
| Mouse: Lfng-CreERT2: B6;D-Tg(Lfng-TagRFP/cre/ERT2)8Amc/J | Jackson Laboratory | JAX: 017496 |
| Mouse: tdTomato: B6;129S6-Gt(ROSA)26Sortm14(CAG-tdTomato)Hze/J | Jackson Laboratory | JAX: 007908 |
|
| ||
| Recombinant DNA | ||
|
| ||
| pTXB1-Tn5 | Addgene | Plasmid #60240 |
| pK19pA-MN | Addgene | Plasmid #86973 |
| pLKO-scramble-H2B-mRFP1;CBFRE-EGFP | Elaine Fuchs (Williams et al., 2011) | NA |
| psPAX2 | Addgene | Plasmid #12260 |
| pCMV-VSV-G | Addgene | Plasmid #8454 |
|
| ||
| Software and Algorithms | ||
|
| ||
| STAR aligner | Dobin et al., 2013 | https://github.com/alexdobin/STAR |
| RSEM | Li and Dewey, 2011 | https://github.com/deweylab/RSEM |
| DESeq2 | Love et al., 2014 | https://bioconductor.org/packages/release/bioc/html/DESeq2.html |
| bedtools | Quinlan and Hall, 2010 | https://bedtools.readthedocs.io/en/latest/ |
| UMI_tools | Smith et al., 2017 | https://github.com/CGATOxford/UMI-tools |
| MACS2 | Feng et al., 2012 | https://github.com/taoliu/MACS |
| ChromHMM | Ernst and Kellis, 2012 | http://compbio.mit.edu/ChromHMM/ |
| IGV | Robinson et al., 2011 | http://software.broadinstitute.org/software/igv/ |
| deepTools | Ramírez et al., 2014 | https://deeptools.readthedocs.io/en/develop/index.html |
| HOMER | Heinz et al., 2010 | http://homer.ucsd.edu/homer/ |
| Tomtom Motif comparison tool | Gupta et al., 2007 | http://meme-suite.org/tools/tomtom |