Antibodies |
|
Mouse monoclonal GAPDH |
Abcam |
ab9484 |
Rabbit polyclonal Requiem |
Sigma |
SAB4502621 |
Mouse monoclonal FLAG |
Sigma |
F1804 |
Rabbit polyclonal TBX3 |
Invitrogen |
42-4800 |
Goat polyclonal OCT4 |
R&D systems |
AF1759 |
Goat polyclonal SOX2 |
R&D systems |
AF2018 |
Mouse monoclonal NESTIN |
BD PharMingen |
556309 |
Mouse monoclonal TUBB3 |
Promega |
G712A |
Rabbit polyclonal NANOG |
Abcam |
Ab80892 |
Mouse monoclonal P300 |
Active motif |
61401 |
Mouse monoclonal STAT3 |
Cell Signaling Technology |
9139 |
Rabbit monoclonal H3K27ac |
Abcam |
ab177178 |
Rabbit polyclonal H3K27me3 |
Millipore |
07449 |
Rabbit polyclonal H3K4me3 |
Abcam |
ab8580 |
Rabbit polyclonal H3K9ac |
Abcam |
ab4441 |
Mouse monoclonal H4-tetraAC |
Active motif |
39967 |
Polyclonal goat SOX17 |
R&D systems |
AF1924 |
Rabbit polyclonal GATA4 |
Santa Cruz |
sc-9053 |
Goat polyclonal GATA6 |
R&D systems |
AF1700 |
Rabbit polyclonal SUZ12 |
Abcam |
ab12073 |
Mouse monoclonal EZH2 |
BD PharMingen |
612667 |
Rabbit polyclonal EED |
Millipore |
17-10034 |
Rabbit monoclonal BRG1 |
Abcam |
ab110641 |
Mouse IgG |
ThermoFisher |
A-11032 |
Alex488-conjugated donkey anti-goat IgG |
ThermoFisher |
A-11055 |
Alex594-conjugated donkey anti-rat IgG |
ThermoFisher |
A-21209 |
Alex488-conjugated donkey anti-mouse IgG |
ThermoFisher |
A-21202 |
Alex594-conjugated donkey anti-rabbit IgG |
ThermoFisher |
A-21207 |
DAPI |
ThermoFisher |
D1306 |
|
Bacterial and Virus Strains |
|
DH5a Competent Cells |
NEB |
C-29871 |
One Shot TOP10 Chemically Competent E. coli
|
ThermoFisher |
C404010 |
|
Chemicals, Peptides, and Recombinant Proteins |
|
LIF |
Millipore |
ESG1107 |
BMP4 |
R&D System |
5020-BP-010 |
Zeocin |
ThermoFisher |
R25001 |
G418 |
ThermoFisher |
11811031 |
Puromycin |
ThermoFisher |
A1113802 |
Protease inhibitors |
Roche |
4693159001 |
Benzonase |
Sigma |
E8263-5KU |
2x Laemmli Sample Buffer |
Bio-Rad |
#1610737 |
3X FLAG peptide |
Sigma |
F4799-4MG |
Trypsin-EDTA (0.25%), phenol red |
ThermoFisher |
25200056 |
Paraformaldehyde |
Sigma |
P6148-500G |
Disuccinimidyl glutarate |
ThermiFisher |
20593 |
Triton X-100 |
Sigma |
T8787-50ML |
4-Hydroxytamoxifen |
TOCRIS |
3412 |
Tamoxifen |
Sigma |
T5648 |
Annexin-APC |
BD PharMingen |
550475 |
7-AAD |
BD PharMingen |
559925 |
SYBR Green PCR Master Mix |
ThermoFisher |
4309155 |
ABsolute QPCR Mix, ROX |
ThermoFisher |
AB1139A |
SequalPrep Long PCR Kit with dNTPs |
ThermoFisher |
A10498 |
Expand Long Template PCR System |
Roche |
03321053103 |
Disuccinimidyl glutarate |
ThermoFisher |
20593 |
Proteinase K |
ThermoFisher |
25530049 |
T4 DNA ligase |
NEB |
M0202S |
Csp6I |
Thermo Fisher |
FD0214 |
MboI |
Thermo |
FD0814 |
Vivaspin500 PES centrifugal filters |
Vivascience |
VS0102 |
KAPA HTP Library Preparation kit |
Roche |
07961901001 |
|
Critical Commercial Assays |
|
AP staining kit |
Sigma |
SCR004 |
SequalPrep Long PCR kit |
Invitrogen |
A10498 |
BCA Protein Assya Kit |
Pierce |
23227 |
ECL Plus |
Amersham |
RPN2133 |
RNeasy mini kit |
QIAGEN |
74104 |
TotalPrep RNA Amplification Kit |
Ambion |
AMIL1791 |
NucleoSpin gDNA Clean-Up kit |
Macherey-Nagel |
740230.10 |
SuperscriptIII reverse transcriptase |
Invitrogen |
18080093 |
Click-iT EdU Pacific Blue flow cytometry Assay Kit |
Invitrogen |
C10636 |
Pierce BCA Protein Assay Kit |
Invitrogen |
23225 |
|
Deposited Data |
|
ChIP-seq |
This study |
E-MTAB-6165 |
RNA-seq |
This study |
E-MTAB-6166 |
4C |
This study |
E-MTAB-6167 |
|
Experimental Models: Cell Lines |
|
E14 ESCs |
This study |
N/A |
R26::CreERT2 - E14 ESCs |
This study |
N/A |
R26::CreERT2 Dpf2 fl/fl E14 ESCs |
This study |
N/A |
Eed −/− R26::CreERT2 Dpf2 fl/fl E14 ESCs |
This study |
N/A |
Ezh2 −/− R26::CreERT2 Dpf2 fl/fl E14 ESCs |
This study |
N/A |
Tbx3 DE KO ESCs |
This study |
N/A |
Tbx3 IE KO ESCs |
This study |
N/A |
|
Experimental Models: Organisms/Strains |
|
SCID mice |
Hans Scholer’s Group |
N/A |
|
Deposited Data |
|
ChIP-seq data |
This study |
E-MTAB-6165 (ArrayExpress) |
RNA-seq data |
This study |
E-MTAB-6166 (ArrayExpress) |
4C data |
This study |
E-MTAB-6167 (ArrayExpress) |
Proteomics data |
This study |
PXD011806 (ProteomeXchange) |
|
Oligonucleotides |
|
Oct4 |
TaqMan |
Mm00658129_gH |
Klf4 |
TaqMan |
Mm00516104_m1 |
Nanog |
TaqMan |
Mm02384862_g1 |
Rex1 |
TaqMan |
Mm03053975_g1 |
Nr0b1 |
TaqMan |
Mm00431729_m1 |
Klf2 |
TaqMan |
Mm01244979_g1 |
Klf5 |
TaqMan |
Mm00456521_m1 |
Gapdh |
TaqMan |
4352339E |
Tbx3 |
TaqMan |
Mm01195726_m1 |
GATA6 |
TaqMan |
Mm00802636_m1 |
GATA4 |
TaqMan |
Mm00484689_m1 |
Sox17 |
TaqMan |
Mm00488363_m1 |
FGF5 |
TaqMan |
Mm00438918_m1 |
Sox1 |
TaqMan |
Mm00486299_s1 |
Pax6 |
TaqMan |
Mm00443072_m1 |
Brachyury |
TaqMan |
Mm01318252_m1 |
Tubb3 |
TaqMan |
Mm00727586_s1 |
Dpf2 |
TaqMan |
Mm00599980_m1 |
Nestin |
TaqMan |
Mm00450205_m1 |
Pdgfra |
TaqMan |
Mm00440701_m1 |
GATA2 |
TaqMan |
Mm00492301_m1 |
Bmp4 |
TaqMan |
Mm00432087_m1 |
Hand1 |
TaqMan |
Mm00433931_m1 |
Sox21 |
TaqMan |
Mm00844350_s1 |
Gjb3 |
TaqMan |
Mm00433647_m1 |
Lama1 |
TaqMan |
Mm01226102_m1 |
Ncam1 |
TaqMan |
Mm01149710_m1 |
Pcdh17 |
TaqMan |
Mm00977568_m1 |
See Table S5 for qPCR and gRNA sequences |
This Study |
N/A |
|
Recombinant DNA |
|
Dpf2 targeting vector |
EUCOMM resource |
N/A |
C-FTAP-tag Dpf2 knockin vector |
This study |
N/A |
pPyCAG-Dpf2-IZ |
Hitoshi Niwa |
N/A |
pPyCAG-Tbx3-IN |
Hitoshi Niwa |
N/A |
pCAGGs-FlpE |
This study |
N/A |
Nanog shRNA |
Wu Qiang |
N/A |
Tbx3 shRNA |
April Kartikasari |
N/A |
|
Reagent or Resource |
|
GMEM |
Sigma-Aldrich |
G2549 |
FCS |
GIBCO |
10439024 |
Non-essential amino acid |
GIBCO |
11140050 |
Sodium pyruvate |
GIBCO |
11360070 |
2-mercaptoethanol |
GIBCO |
21985023 |
L-glutamine |
GIBCO |
25030081 |
TCEP |
Sigma |
75259 |
Iodoacetamide |
Sigma |
I6125 |
colloidal Coomassie |
Sigma |
B2025 |
AggreWell 400 plates |
STEMCELL Technoligies |
34421 |
Dynabeads Protein G |
Invitrogen |
10003D |
4-12% Bis-Tris Novex gel |
Invitrogen |
NP0321BOX |
PVDF membranes |
Biorad |
1620177 |
|
Software and Algorithms |
|
ChromHMM v1.1.0 |
Chronis et al., 2017 |
N/A |
Bowtie2 v2.2.1 |
Langmead et al., 2009 |
N/A |
Cufflinks v2.2.1 |
Trapnell et al., 2010 |
N/A |
MACS2 v20140616 |
Zhang et al., 2008 |
N/A |
BedTools v2.27 |
Quinlan and Hall, 2010 |
N/A |
HOMER v4.9.0 |
Heinz et al., 2010 |
N/A |
Metascape |
http://metascape.org |
N/A |
Proteome Discover 1.4 |
Thermofisher |
N/A |
Tophat version 2.0.13 |
Trapnell et al., 2009 |
N/A |
Mascot 2.5 |
Matrix Science |
N/A |