| Antibodies |
|
|
| Biotin anti-mouse TER-119 |
BioLegend |
AB_313705 |
| Biotin anti-mouse CD45 |
BioLegend |
AB_312969 |
| Biotin anti-mouse CD31 |
BioLegend |
AB_312899 |
| PerCP/Cy5.5 anti-mouse/human CD49f |
BD Biosciences |
AB_11151910 |
| APC anti-mouse CD326 (Ep-CAM) |
BioLegend |
AB_1134102 |
| PE/Cy7 anti-mouse Ly-6A/E (Sca-1) |
BioLegend |
AB_493596 |
| PE Streptavidin |
BioLegend |
AB_2819020 |
| Streptavidin V450 |
BD Biosciences |
AB_2033992 |
| Sox9 (D8G8H) Rabbit mAb |
Cell Signaling Technology |
AB_2665492 |
| Rabbit Anti-Histone H3 |
Abcam |
AB_302613 |
| HRP Goat anti-mouse IgG |
BioLegend 405306 |
AB_315009 |
| HRP Goat anti-mouse IgG |
BioLegend 406401 |
AB_2099368 |
| Rabbit Purified anti-Keratin 14 Antibody |
Biolegend 905304 |
AB_2616896 |
| Chicken Purified anti-Keratin 14 Antibody |
Biolegend 906004 |
AB_2616962 |
| Rat Anti-Keratin 8 (Provided as Supernatant) |
Developmental Studies Hybridoma Bank |
AB_531826 |
| Calponin 1 (D8L2T) XP |
Cell Signaling Technology |
AB_2798789 |
| Goat anti-Rat IgG (H+L) Secondary Antibody, Alexa Fluor® 568 conjugate |
ThermoFisher |
AB_2534121 |
| Alexa Fluor® 488-AffiniPure Goat Anti-Chicken IgY (H+L) |
Jackson ImmunoResearch |
AB_2337390 |
| Alexa Fluor® 488-AffiniPure Goat Anti-Rabbit IgG (H+L) |
Jackson ImmunoResearch |
AB_2338046 |
| Goat anti-Rabbit IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 647 |
ThermoFisher |
AB_2535812 |
| Goat anti-Rat IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 546 |
ThermoFisher |
AB_2534125 |
| Bacterial and Virus Strains |
|
|
| ElectroMAX Stbl4 Competent Cells |
ThermoFisher |
Cat# 11635018 |
| Chemicals, Peptides, and Recombinant Proteins |
|
|
| Y-27632 |
Cayman Chemical |
10005583 |
| Phosphate-Buffered Saline, 1X without calcium and magnesium, pH 7.4 ± 0.1 |
Corning |
21-040-CM |
| UltraPureTM 0.5M EDTA, pH 8.0 |
ThermoFisher |
15575020 |
| Human Recombinant Epidermal Growth Factor |
Sigma |
E9644 |
| Human Recombinant Fibroblast Growth Factor 2 |
EMD Millipore |
GF003 |
| Ethanol |
Decon Laboratories, Inc. |
2701 |
| Chloroform |
Fisher Scientific |
BP1145 |
| Glacial Acetic Acid |
Fisher Scientific |
A38S500 |
| 1M Tris-HCl, pH 8.0 |
TekNova |
T1080 |
| Magnesium Chloride Hexahydrate |
Fisher Scientific |
BP214-500 |
| Calcium Chloride |
Fisher Scientific |
BP510-500 |
| EGTA |
Sigma |
E3889 |
| Nonidet P-40 Substitute |
IBI Scientific |
IB01140 |
| Sodium Deoxycholate |
Sigma |
30970 |
| Sodium Fluoride |
Alfa Aesar |
11561-30 |
| b-glycerophosphate disodium salt hydrate |
Sigma |
G9422 |
| Sodium Orthovanadate |
Sigma |
S6508 |
| Halt™ Protease Inhibitor Cocktails |
ThermoFisher |
PI87786 |
| Red Blood Cell Lysing Buffer Hybri-Max |
Sigma |
R7757 |
| Heparin |
Sigma |
H3149 |
| Collagenase 3 |
Worthington |
LS004182 |
| DNase I |
Worthington |
LS002139 |
| 0.05% Trypsin-EDTA |
ThermoFisher |
25300054 |
| Dispase |
Worthington |
LS02109 |
| 3.2% paraformaldehyde |
EMS |
15714 |
| Triton X-100 |
Fisher Scientific |
BP151 |
| Matrigel |
Corning |
354234 |
| Polybrene |
EMD-Millipore |
TR-1003-G |
| Xylenes |
Fisher Scientific |
X3P-1GAL |
| Permount |
Fisher Scientific |
SP15100 |
| Trizol LS |
ThermoFisher |
10296010 |
| TCEP |
GoldBio |
TCEP1 |
| TruPAGE Tris-MOPS SDS Express Running Buffer |
Sigma |
PCG2003 |
| Western Lightning ECL Pro |
PerkinElmer |
NEL121001EA |
| VisiGlo Prime HRP Chemiluminescent ECL Substrate |
Amresco |
89424-016 |
| Methanol |
EMD Millipore |
MX04881 |
| 30% Hydrogen Peroxide |
Fisher Scientific |
NC0512932 |
| Antigen Unmasking Solution |
Vector Laboratories |
H-3300 |
| Lenti-X Concentrator |
Takara |
631232 |
| DAB Peroxidase (HRP) Substrate Kit, 3,3′-diaminobenzidine |
Vector Laboratories |
SK-4100 |
| Critical Commercial Assays |
|
|
| High-Capacity cDNA Reverse Transcription Kit |
ThermoFisher |
4368813 |
| Power SYBR® Green PCR Master Mix |
ThermoFisher |
4368708 |
| PrimeSTAR MAX DNA polymerase |
Takara |
R045A |
| NEB HiFi Assembly Kit |
New England Biolabs |
E2621S |
| Qubit® RNA HS Assay Kit |
ThermoFisher |
Q3285 |
| Affymetrix Clariom S Pico, Mouse |
ThermoFisher |
902932 |
| TruPAGE Precast Gels |
Sigma |
PCG3003 |
| Nextera DNA Library Kit |
Illumina |
FC-121-1030 |
| Deposited Data |
|
|
| Sox9-GFP; C3(1)-Tag Microarray Data, Sox9-cKO Microarray Data, and Sox9-GFP; C3(1)-Tag ATAC-seq Data |
GEO |
GEO: GSE135892
|
| Experimental Models: Cell Lines |
|
|
| Sox9-Flox Mammary Epithelial Organoids |
This Paper |
N/A |
| Rosa26-Cas9-EGFP Mammary Epithelial Organoids |
This Paper |
N/A |
| HEK293T cell line, ATCC |
ATCC |
CVCL_0063 |
| Experimental Models: Organisms/Strains |
|
|
| B6.129S7-Sox9tm2Crm/J Mus musculus
|
JAX |
IMSR_JAX:013106 |
| FVB-Tg(C3-1-TAg)cJeg/JegJ Mus musculus
|
JAX |
IMSR_JAX:013591 |
| B6J.129(Cg)-Gt(ROSA)26Sortm1.1(CAG-cas9*,-EGFP)Fezh/J Mus musculus
|
JAX |
IMSR_JAX:026179 |
| FVB-Tg(MMTV-iCre/CAG-CAC-ECFP) Mus musculus
|
Pollard Lab |
Roussos et al., 2010 |
| STOCK Tg(Sox9-EGFP)EB209Gsat/Mmucd Mus musculus
|
MMRRC |
MMRRC_011019-UCD |
| FVBJ.B6(Cg) Tg(Sox9-EGFP)EB209Gsat/Mmucd Mus musculus
|
This Paper |
N/A |
| FVB-Tg(MMTV-iCre/CAG-CAC-ECFP); B6.129S7-Sox9tm2Crm/J Mus musculus
|
This Paper |
N/A |
| FVB-Tg(MMTV-iCre/CAG-CAC-ECFP); B6.129S7-Sox9tm2Crm/J; FVB-Tg(C3-1-TAg)cJeg/JegJ Mus musculus
|
This Paper |
N/A |
| FVB-Tg(C3-1-TAg)cJeg/JegJ; FVBJ.B6(Cg) Tg(Sox9-EGFP)EB209Gsat/Mmucd Mus musculus
|
This Paper |
N/A |
| Oligonucleotides |
|
|
| Primers for genotyping are found in the genotyping primers table |
Multiple Sources |
N/A |
| Primers for RT-PCR are found in the RT-PCR primers table |
This Paper |
N/A |
| Primers for cloning are found in the cloning primers table |
This Paper |
N/A |
| Recombinant DNA |
|
|
| pBabe puro IkB alpha M |
Addgene |
Addgene_12332 |
| pLVX-Puro |
Takara |
632164 |
| pMD2.G |
Addgene |
Addgene_12259 |
| pCMVR8.74 |
Addgene |
Addgene_22036 |
| pLVX-Puro-IKBKBMut
|
This Paper |
N/A |
| pXLV-Puro |
Zhang et al., 2016 |
N/A |
| pXLV-sgNT1 |
This Paper |
N/A |
| pXLV-Puro sgSox9 |
This Paper |
N/A |
| pXLV-Puro sgNfkb2 E2 |
This Paper |
N/A |
| pXLV-Puro sgNfkb2 E5 |
This Paper |
N/A |
| Software and Algorithms |
|
|
| TAC V4.0 |
Thermofisher |
N/A |
| FlowJo VX |
BD |
N/A |
| GSEA 3.0 |
Mootha et al., 2003; Subramanian et al., 2005
|
N/A |
| Seurat V3.0 |
Stuart et al., 2019 |
N/A |
| Bowtie v1.2 |
Langmead et al., 2009 |
N/A |
| preprocessCore v1.46 |
GenePattern Server |
N/A |
| deepTools v2.0 |
Ramírez et al., 2014 |
N/A |
| SICER-df-rb v1.1 |
Zang et al., 2009 |
N/A |
| BD FACSDiva V8 |
BD |
N/A |
| chromVAR |
Schep et al., 2017 |
N/A |
| Other |
|
|
| EpiCult™-B Mouse Medium Kit |
Stem Cell Technologies |
05610 |
| Fetal Bovine Serum, Heat Inactivated |
Corning |
35-015-CV |
| DMEM/F12 |
Corning |
10-092-CV |
| AMPure XP beads |
Beckman |
A63881 |
