Key resources table.
| Reagent type (species) or resource |
Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Genetic reagent (M. musculus) | Gli3Xt-J Gli3+/- | Jackson Laboratory | Jackson Cat# 000026, MGI Cat# 2169581, RRID:MGI:2169581 |
Obtained from the Laboratory of Dr. Andy McMahon |
| Genetic reagent (M. musculus) |
Shhtm1amc Shh+/- | Jackson Laboratory | Jackson Cat# 003318, MGI Cat# 3584154, RRID:MGI:3584154 |
Obtained from the Laboratory of Dr. Andy McMahon |
| Genetic reagent (M. musculus) | Gli3FLAG | Laboratory of Dr. Andy McMahon | Obtained from the Laboratory of Dr. Andy McMahon | |
| Genetic reagent (M. musculus) | Swiss Webster Wildtype |
Charles River | Charles River Cat# NCI 551 IMSR Cat# TAC:sw, RRID:IMSR_TAC:sw |
|
| Cell line | NIH 3T3 | ATCC | Cat# CRL-6442, RRID:CVCL_0594 | Used for conventional ChIP-seq |
| Antibody | Anti-H3K27ac (mouse mono-clonal) | Diagenode | Diagenode Cat# C15200184, RRID:AB_2713908 | Used for conventional ChIP-seq |
| Antibody | Anti-H3K27ac (rabbit polyclonal) | Abcam | Abcam Cat# ab4729, RRID:AB_2118291 | Used for conventional ChIP-qPCRs |
| Antibody | Anti-H3K27ac (rabbit polyclonal) | Diagenode | Diagenode Cat# C15410196, RRID:AB_2637079 | Used for conventional MicroChIP-seq |
| Antibody | Anti-H3K27me3 (rabbit polyclonal) | Abcam | Abcam Cat# Ab195477, RRID:AB_2819023 |
Used for conventional ChIP-seq |
| Antibody | Anti-H3K4me1 (rabbit polyclonal) | Millipore | Millipore Cat# 07–436, RRID:AB_310614 | Used for conventional ChIP-qPCRs |
| Antibody | Anti-H3K4me2 (rabbit polyclonal) | Millipore | Millipore Cat# 07–030, RRID:AB_11213050 | Used for conventional ChIP-seq |
| Antibody | Anti-M2 FLAG (mouse monoclonal) | Sigma | Sigma-Aldrich Cat# F3165, RRID:AB_259529 | Used for conventional ChIP-seq and WB (1:4000) |
| Antibody | Anti-HDAC1 (rabbit polyclonal | Abcam | Abcam Cat# ab7028, RRID:AB_305705 | Used for conventional ChIP-seq |
| Antibody | Anti-Histone H3 (rabbit polyclonal | Cell Signaling Technology |
Cell Signaling Technology Cat# 4499, RRID:AB_10544537 | Used for WB (1:4000) |
| Antibody | Anti-GAPDH (rabbit polyclonal | Cell Signaling Technology |
Cell Signaling Technology Cat# 5174, RRID:AB_10622025 | Used for WB (1:1000) |
| Antibody | Anti-B-actin (rabbit polyclonal | Cell Signaling Technology |
Cell Signaling Technology Cat# 8457, RRID:AB_10950489 | Used for WB (1:2000) |
| Antibody | Donkey-anti-mouse | Jackson Immuno-Research | Jackson ImmunoResearch Labs Cat# 715-035-150, RRID:AB_2340770 | Used for WB (1:5000) |
| Antibody | Donkey-anti-rabbit | Jackson Immuno-Research | Jackson ImmunoResearch Labs Cat# 711-005-152, RRID:AB_2340585 | Used for WB (1:5000) |
| Antibody | Dynabeads M-280 Sheep Anti-Mouse IgG | Invitrogen, Thermo Fisher Scientific | Thermo Fisher Scientific Cat# 11201D, RRID:AB_2783640 | |
| Antibody | Dynabeads M-280 Sheep Anti-Rabbit IgG | Invitrogen, Thermo Fisher Scientific |
Thermo Fisher Scientific Cat# 11203D, RRID:AB_2783009 |
|
| Chemical compound, drug | Purmorphamine | Stemgent | Stemgent Cat# 04–0009 | Used in cell culture (400 nM) |
| Chemical compound, drug | SAHA | Selleckchem | Selleckchem Cat# MK0683 | Used in limb bud culture (20 μM) |
| Chemical compound, drug | FK228 | Selleckchem | Selleckchem Cat# S3020 | Used in limb bud culture (250 nM) |
| Commercial Assay or Reagent | SensiFAST SYBR-LoROX | Bioline | Bioline Cat# BIO-94020 | |
| Commercial Assay or Reagent | NEBNext DNA Library Prep Master Mix Set for Illumina | New England Biolabs | NEB Cat# E6040L, E7645L | |
| Commercial Assay or Reagent | Agencourt AMPure XP | Beckman Coulter | Beckman Coulter Cat# A63881 | |
| Commercial Assay or Reagent | True MicroChIP Kit | Diagenode | Diagenode Cat# C01010130 | |
| Commercial Assay or Reagent | MicroPlex Library Prep Kit | Diagenode | Diagenode Cat# C05010012 | |
| Commercial Assay or Reagent | Liberase | Roche | Roche Cat# 05401119001 | Cell dissociation (100 µg/mL) |
| Software, Tools | MACS version 2.1.0 | (Zhang et al., 2008https://github.com/taoliu/MACS | MACS, RRID:SCR_013291 | |
| Software, Tools | limma | (Ritchie et al., 2015) | LIMMA, RRID:SCR_010943 | http://bioconductor.org/packages/release/bioc/html/limma.html |
| Software, Tools | R statistical software | (R Development Core Team, 2014) | R Project for Statistical Computing, RRID:SCR_001905 | https://www.r-project.org/ |
| Software, Tools | CisGenome | (Ji et al., 2008) | CisGenome, RRID:SCR_001558 | http://www.biostat.jhsph.edu/~hji/cisgenome/ |
| Database, Tools | JASPAR motif database | (Khan et al., 2018) | JASPAR, RRID:SCR_003030 | http://jaspar.genereg.net/ |
| Database, Tools | Transfac motif database | (Matys et al., 2006) | TRANSFAC, RRID:SCR_005620 | http://gene-regulation.com/pub/databases.html |
| Database, Tools | VISTA enhancer browser | (Visel et al., 2007) | VISTA Enhancer Browser, RRID:SCR_007973 | https://enhancer.lbl.gov/ |