KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| anti-EGFR mouse monoclonal (3C6) | Roche | Cat#790-2988; RRID:AB_2335974 |
| anti-MEOX2 rabbit polyclonal | Sigma Aldrich | Cat#HPA053793; RRID:AB_2682264 |
| anti-MYF5 mouse monoclonal (OTI2G5) | Invitrogen | Cat#MA5-26654; RRID:AB_2724766 |
| anti-MYOG mouse monoclonal (F5D) | Agilent | Cat#M3559; RRID:AB_2250893 |
| PE/Cy7-conjugated anti-EGFR human monoclonal (AY13) | BioLegend | Cat#352910; RRID: AB_2562159 |
| Bacterial and Virus Strains | ||
| ElectroMAX Stbl4 E. coli cells | Thermo Fischer Scientific | Cat#11635018 |
| Biological Samples | ||
| Frozen patient tumors | St. Jude Children’s Research Hospital Biorepository | In this study |
| Orthotopic patient-derived xenografts (O-PDXs) | St. Jude Children’s Research Hospital Childhood Solid Tumor Network (CSTN) | https://cstn.stjude.cloud/ |
| Fixed matched pairs of tumor samples (before and mid-treatment) | RMS13 clinical trial (NCT01871766) | In this study |
| Chemicals, Peptides, and Recombinant Proteins | ||
| TaqMan Fast Advanced Master Mix | Invitrogen | Cat#4444965 |
| DMEM media | Thermo Fischer Scientific | Cat#11960044 |
| SkBM-2 skeletal muscle media BulletKit | Lonza | Cat#CC-3245 |
| CellTiter-Glo 3D | Promega | Cat#G9681 |
| Vincristine, 2mg/2ml | Hospira | NDC #61703-309-16; CAS 57-22-7 |
| Irinotecan, 40mg/2ml | Pfizer | NDC #0009-7529-04; CAS 100286-90-6 |
| SN-38 | TCI Chemicals | Cat#E0748; CAS 86639-52-3 |
| Gefitinib | MedChemExpress | Cat#HY50895; CAS 184475-35-2 |
| Afatinib | MedChemExpress | Cat#HY10261; CAS 850140-72-6 |
| Critical Commercial Assays | ||
| Chromium Single Cell 3’ Gene Expression ReagentKit (v2 or v3) | 10x Genomics | Cat#PN-120237 (v2) or #PN-1000075 (v3) |
| Chromium Single Cell A Chip Kit (for v2 gene expression) | 10x Genomics | Cat#PN-120236 |
| Chromium Single Cell A Chip Kit (for v3 gene expression) | 10x Genomics | Cat#PN-1000153 |
| Chromium i7 Multiplex Primers | 10x Genomics | Cat#PN-120262 |
| Chromium Single Cell ATAC Library & Gel Bead Kit | 10x Genomics | Cat#PN-1000110 |
| Chromium Chip E Single Cell ATAC Kit | 10x Genomics | Cat#PN-1000155 |
| Chromium i7 Multiplex Kit N, Set A (for scATAC-seq) | 10x Genomics | Cat#PN-1000084 |
| 3’ CellPlex Kit Set A (for multiplexed scRNA-seq) | 10x Genomics | Cat#PN-1000261 |
| Papain Dissociation System | Worthington Biochemicals | Cat#LK003150 |
| PCR Purification Kit | Qiagen | Cat#28104 |
| High Capacity RNA-to-DNA kit | Invitrogen | Cat#4387406 |
| Deposited Data | ||
| Mouse Organogenesis Cell Atlas | (Cao et al., 2019) | https://oncoscape.v3.sttrcancer.org/mouse |
| Single-cell/nucleus RNA-seq data | This study | GEO GSE174376 |
| Experimental Models: Cell Lines | ||
| HEK293T | ATCC | RRID: CVCL_0063 |
| Experimental Models: Organisms/Strains | ||
| Mouse: Nude: NCI Athymic NCr-nu/nu | Charles River Laboratories | strain 553 |
| Mouse: NSG: NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ | Jackson Laboratories | strain 005557 |
| Oligonucleotides | ||
| Barcode dialout PCR-F | Integrated DNA Technologies | 5’-TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGCTACACGACGCTCTTCCGAT-3’ |
| Barcode dialout PCR-R | Integrated DNA Technologies | 5’-GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGTAGCAAACTGGGGCACAAGC-3’ |
| Recombinant DNA | ||
| pBA439 barcode library | Addgene | Cat#85968; RRID:Addgene_85968 |
| Software and Algorithms | ||
| UMI-tools | (Smith et al., 2017) | https://github.com/CGATOxford/UMI-tools |
| R | CRAN | https://cran.r-project.org/ |
| RStudio | RStudio | https://www.rstudio.com/ |
| CellRanger v3.0.2 | 10x Genomics | https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome |
| Seurat v3.1.2 | (Butler et al., 2018; Stuart et al., 2019) | https://satijalab.org/seurat/ |
| Sctransform v0.2.1 | (Hafemeister and Satija, 2019) | https://github.com/ChristophH/sctransform |
| velocyto v0.17.17 | (Manno et al., 2018) | http://velocyto.org/ |
| Scanpy v1.4.5 | (Wolf et al., 2018) | https://github.com/theislab/scanpy |
| scVelo v0.1.24be | (Bergen et al., 2020) | https://github.com/theislab/scvelo |
| SingleR v1.0.1 | (Aran et al., 2019) | https://github.com/dviraran/SingleR |
| inferCNV v1.1.3 | Trinity CTAT project | https://github.com/broadinstitute/infercnv |
| Conos v1.2.1 | (Barkas et al., 2019) | https://github.com/kharchenkolab/conos |
| dynverse | (Saelens et al., 2019) | https://dynverse.org/ |
| Slingshot | (Street et al., 2018) | https://github.com/kstreet13/slingshot |
| CellRanger ATAC v1.2.0 | 10x Genomics | https://support.10xgenomics.com/single-cell-atac/software/overview/welcome |
| Signac v1.1.0 | (Stuart et al., 2021) | https://satijalab.org/signac/ |
| Latent cellular analysis | (Cheng et al., 2019) | https://bitbucket.org/scLCA/single_cell_lca/src |
| NetBID | (Du et al., 2018) | https://github.com/jyyulab/NetBID |
| SJARACHNe | (Khatamian et al., 2018) | https://github.com/jyyulab/SJARACNe |
| Prism software v9.0 | GraphPad | https://www.graphpad.com/ |
| FCS Express v7 | De Novo Software | https://denovosoftware.com/ |