KEY RESOURCES TABLE.
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| AMV-3C2 Monoclonal Antibody (supernatant) | Developmental Studies Hybridoma Bank | AMV-3C2 |
| Bacterial and virus strains | ||
| RCASBP(A)-deltaF1’ | Dr. Stephen Hughes’ Laboratory, NCI-NIH, Bethesda | Replication competent RCAS virus |
| RCASBP(A)-deltaF1’::GFP | Dr. Stephen Hughes’ Laboratory, NCI-NIH, Bethesda | Replication competent RCAS virus expressing GFP |
| Biological samples | ||
| Chemicals, peptides, and recombinant proteins | ||
| OCT compound | Sakura Inc. | Ref# 4582 |
| DMEM (High Glucose) Media | ATCC | Cat# 30–2002 |
| DMEM (GlutaMAX, High Glucose, HEPES) Media | Gibco/Thermo Fisher | Cat# 10564011 |
| Collagenase Type II | Gibco | Ref# 17101–015 |
| Hyaluronidase Type IV-S | Sigma Life Sciences | Cat# H4272 |
| Proteinase K | Qiagen | Cat# 19131 |
| Hematoxylin Gill-1 | Ricca Chemical Company | Cat# 3535–32 |
| Ammonium Hydroxide Solution | Sigma Aldrich | Cat# 221228 |
| Ampure XP magnetic beads | Beckman Coulter | Ref# A63880 |
| Mag-Bind Rxn Pure Plus magnetic beads | Omega Bio-Tek | Cat# 1386 |
| MyTaq Red PCR Mix | Bioline/Meriadian BioScience | Cat# BIO-25044 |
| Superscript II Reverse Transcriptase | Invitrogen | Cat# 18064014 |
| Sso Advanced SYBR Green Supermix | BioRad | Cat# 1725271 |
| NEBNext High-Fidelity PCR MasterMix | New England Biolabs | Cat# M0541 |
| Q5 High-Fidelity Mastermix | New England Biolabs | Cat# M0492 |
| Critical commercial assays | ||
| Jerboa Shox2 in situ Probe | Advanced Cell Diagnostics Inc. | Part ID 578821 |
| Jerboa Mab21L2 in situ Probe | Advanced Cell Diagnostics Inc. | Part ID 723661 |
| Jerboa Gdf10 in situ Probe | Advanced Cell Diagnostics Inc. | Part ID 578801 |
| Jerboa Pax1 in situ Probe | Advanced Cell Diagnostics Inc. | Part ID 578851 |
| Jerboa HoxB13 in situ Probe | Advanced Cell Diagnostics Inc. | Part ID 578841 |
| Jerboa HoxB9 in situ Probe | Advanced Cell Diagnostics Inc. | Part ID 1072041 |
| Jerboa Prrx1 in situ Probe | Advanced Cell Diagnostics Inc. | Part ID 1072031 |
| Mouse Galnt17 in situ Probe | Advanced Cell Diagnostics Inc. | Part ID 579031 |
| Mouse Shox2 in situ Probe | Advanced Cell Diagnostics Inc. | Part ID 579051 |
| Mouse Mab21L2 in situ Probe | Advanced Cell Diagnostics Inc. | Part ID 456901 |
| Mouse Gdf10 in situ Probe | Advanced Cell Diagnostics Inc. | Part ID 525161 |
| Mouse Pax1 in situ Probe | Advanced Cell Diagnostics Inc. | Part ID 579091 |
| Mouse HoxB13 in situ Probe | Advanced Cell Diagnostics Inc. | Part ID 579101 |
| Mouse HoxB9 in situ Probe | Advanced Cell Diagnostics Inc. | Part ID 452821 |
| Mouse Prrx1 in situ Probe | Advanced Cell Diagnostics Inc. | Part ID 485231 |
| Mouse Galnt17 in situ Probe | Advanced Cell Diagnostics Inc. | Part ID 578861 |
| Protease Plus Solution | Advanced Cell Diagnostics Inc. | Part ID 322331 |
| Protease III Solution | Advanced Cell Diagnostics Inc. | Part ID 322337 |
| RED Chromogenic in situ staining and Detection Kits |
Advanced Cell Diagnostics Inc. | Part ID 322350 Part ID 323971 |
| TruSeq Stranded RNA Library Preparation Kit | Illumina Inc. | RS-122-2101 |
| Nextera DNA Sample Preparation Kit | Illumina Inc. | FC-121-1030 |
| Deposited data | ||
| RNA-Seq fastq illumina sequencing reads for Mouse and Jerboa cartilage samples | This paper | Zenodo |
| ATAC-Seq fastq illumina sequencing reads for Mouse and Jerboa cartilage samples | This paper | Zenodo |
| DESeq2 R-Script and associated library used for differential expression analysis | This paper | Zenodo |
| RNA in situ hybridization for Galnt17 in mouse and jerboa growth cartilages. | This paper | Zenodo |
| DESeq2 MA-plot for Jerboa and Mouse metatarsal comparison | This paper | Zenodo |
| Data tables with STAR gene counts and DESeq2 differential expression results for all of the 17,464 mouse and jerboa orthologous. | This paper | Zenodo |
| Experimental models: Cell lines | ||
| DF-1 Chicken Fibroblast Cells | Dr. Clifford J. Tabin’s Laboratory, Harvard University | N/A |
| Experimental models: Organisms/strains | ||
| Mus musculus (CD-1 Strain) | Charles River Labs | N/A |
| Jaculus jaculus | Dr. Kim Cooper’s Lab | N/A |
| Gallus gallus (SPF eggs; White Leghorn Strain) | Charles River Labs | N/A |
| Oligonucleotides | ||
| Fwd (5’-3’): AGAGCTCCGCAGAAAGCGAC Rev (5’-3’): GCGTCTTCAGCACCGAGAGG | This Study | Mouse Mab21L2, qRT-PCR primers |
| Fwd (5’-3’): ACCGCGACGTGGTCAAGATG Rev (5’-3’): CAGGGGATATGGGGCATGGG | This Study | Jerboa Mab21L2, qRT-PCR primers |
| Fwd (5’-3’): ACGGAGGTGTCCCCTGAACT Rev (5’-3’): CGCCTCTGCTTGATTTTGGT | Cobb & Duboule108 | Mouse Shox2, qRT-PCR primers |
| Fwd (5’-3’): AAAGGTGTTCTCATAGGGGCTGCT Rev (5’-3’):CGTCACGTTGCAATGACTATCCTGC | This Study | Jerboa Shox2, qRT-PCR primers |
|
Fwd1 (5’-3’): GTTTGCAGAGCCCAGTGTCC. Rev1 (5’-3’): GATAGCCCCGAGGAACAGTC Fwd2 (5’-3’): CAACGCTGATGCCAACTGTC. Rev2 (5’-3’): GACACTGGGCTCTGCAAAC |
This Study | Mouse HoxB13, PCR primers |
| Fwd (5’-3’): CAGGAGGGGGTCGGAATCTA Rev (5’-3’): GCACGCTCGACTCTGCAAAT | This Study | Jerboa HoxB13, PCR primers |
| Fwd (5’-3’): GGAACACTCCAAAAACAGACCT Rev (5’-3’): CCACCACTGGGTATTGAGTAG | This Study | Mouse Sdha, qRT-PCR primers |
| Fwd (5’-3’): ACTGGAGGTGGCATTTCTAC Rev (5’-3’): TTTTCTAGCTCGACCACAGATG | This Study | Jerboa Sdha, qRT-PCR primers |
| Recombinant DNA | ||
| Software and algorithms | ||
| JMP | SAS Institute Inc. | N/A |
| DESEQ2 | https://bioconductor.org/packages/release/bioc/html/DESeq2.html | N/A |
| STAR | https://github.com/alexdobin/STAR | N/A |
| Ingenuity Pathway Analysis | Qiagen | N/A |
| CESAR | https://github.com/hillerlab/CESAR | N/A |
| liftOver | https://genome.ucsc.edu/cgi-bin/hgLiftOver | N/A |
| Other | ||