Antibodies |
anti-mouse ASCL1 |
Abcam |
ab74065 |
anti-human H2B |
Abcam |
ab1790 |
anti-human H3 |
Abcam |
ab1791 |
Cy5-dCTP |
GE Healthcare Life Sciences |
PA55021 |
Klenow Fragment (3ÅL→5ÅL
exo-) |
New England Biolabs |
M0212S |
Bacterial and Virus Strains |
6HIS_pRSF_TEV |
Gifft from Ronen Marmorstein lab |
6HIS_pRSF_TEV |
FUW-TetO-Gata4 |
Buganim et
al., 2012 |
Addgene 41084 |
pCMW-SPORT6-Hnf1 |
Dharmacon mammalian gene collection |
MMM1013–202761012 |
Tet-O-FUW-Ascl1 |
Vierbuchen et
al., 2010 |
Addgene 27150 |
pBABE-E12-cTAP |
Yang et al.,
2009 |
Addgene 20916 |
pET-28b-FoxA1 |
This paper |
pET-28b-FoxA1 |
pET-28b-Gata4 |
This paper |
pET-28b-Gata4 |
pET-28b-Hnf1a |
This paper |
pET-28b-Hnf1a |
pET-28b-Ascl1 |
This paper |
pET-28b-Ascl1 |
pET-28b-Tcf3 |
This paper |
pET-28b-Tcf3 |
pRSFDUET1-Ascl1+Tcf3 |
This paper |
pRSFDUET1-Ascl1+Tcf3 |
pET-28d-Brn2 |
Gift from Marius Wernig |
pET-28d-Brn2 |
pET-28b-Spi1 |
This paper |
pET-28b-Spi1 |
pET-28b-Cebpa |
This paper |
pET-28b-Cebpa |
pET-28b-Cebpb |
This paper |
pET-28b-Cebpb |
pET-28b-Cebpb-T167D |
This paper |
pET-28b-Cebpb-T167D |
pET-28b-Cebpb- S163D,T167D |
This paper |
pET-28b-Cebpb- S163D,T167D |
Biological Samples |
|
|
|
|
|
Chemicals, Peptides, and
Recombinant Proteins |
His6x-FOXA1 |
This paper |
His6x-FOXA1 |
His6x-GATA4 |
This paper |
His6x-GATA4 |
His6x-HNF1α |
This paper |
His6x-HNF1α |
His6x-ASCL1 |
This paper |
His6x-ASCL1 |
His6x-E12α |
This paper |
His6x-E12α |
His6x-ASCL1/E12α |
This paper |
His6x-ASCL1/E12α, |
GST-His6x-BRN2 |
This paper |
GST-His6x-BRN2 |
His6x-PU1 |
This paper |
His6x-PU1 |
His6x-CEBPα |
This paper |
His6x-CEBPα |
His6x-CEBPβ WT |
This paper |
His6x-CEBPβ WT |
His6x-CEBPβ T167D |
This paper |
His6x-CEBPβ T167D |
His6x-CEBPβ S163D,T167D |
This paper |
His6x-CEBPβ S163D,T167D |
GST-MYOG |
Hu et al.,
2013 |
GST-MYOG |
GST-TBX20 |
Hu et al.,
2013 |
GST-TBX20 |
GST-NHLH2 |
Hu et al.,
2013 |
GST-NHLH2 |
GST-CREM1 |
Hu et al.,
2013 |
GST-CREM1 |
GST-IRF3 |
Hu et al.,
2013 |
GST-IRF3 |
GST-RBPJ |
Hu et al.,
2013 |
GST-RBPJ |
GST-HMGN1 |
Hu et al.,
2013 |
GST-HMGN1 |
GST-HMGN5 |
Hu et al.,
2013 |
GST-HMGN5 |
GST-HMGA1 |
Hu et al.,
2013 |
GST-HMGA1 |
GST-SOX5 |
Hu et al.,
2013 |
GST-SOX5 |
Critical Commercial Assays |
MinElute PCR purification kit |
QIAGEN |
28004 |
Quick change II XL Site-Directed mutagenesis
Kit |
Agilent |
200521 |
Deposited Data |
ASCL1 and BRN2 ChIP-seq |
Vierbuchen et al., 2013 |
GEO GSE43916
|
PU1, CEBPα and CEBPβ
ChIP-seq |
Heinz et al.,
2010 |
GSE21512 |
FOXA1 and HNF1α ChIP-seq |
Faure et al.,
2012 |
E-MTAB-941 |
GATA4 ChIP-seq |
Zheng et al.,
2013 |
GSE49132 |
Fibroblast MNase-seq |
Teif et al.,
2012 |
GSE40910 |
FOXA3-DBD:DNA co-crystal structure |
Clark et al.,
1993 |
RCSB PDB 1VTN |
OCT4-DBD:DNA co-crystal structure |
Esch et al.,
2013 |
RCSB PDB 3L1P |
PU1-DBD:DNA co-crystal structure |
Kodandapani et
al., 1996 |
RCSB PDB 1PUE |
KLF4-DBD:DNA co-crystal structure |
Schuetz et
al., 2011 |
RCSB PDB 2WBS |
GATA3-DBD:DNA co-crystal structure |
Chen et al.,
2012 |
RCSB PDB 4HC9 |
ASCL1 |
SWISS-MODEL |
SMR P50553
|
cMYC/MAX-DBD:DNA co-crystal structure |
Nair and
Burley, 2003 |
RCSB PDB 1NKP |
CEBPα-DBD:DNA co-crystal structure |
Miller et al.,
2003 |
RCSB PDB 1NWQ |
USF-DBD:DNA co-crystal structure |
Ferre-D’Amare et al., 1994 |
RCSB PDB 1AN4 |
MYOG |
SWISS-MODEL |
SMR P15173
|
CREM |
SWISS-MODEL |
SMR Q03060
|
TBX1-DBD:DNA co-crystal structure |
El Omari et
al., 2012 |
RCSB PDB 4A04 |
Brachyury-DBD:DNA co-crystal structure |
Muller and
Herrmann, 1997 |
RCSB PDB 1XBR |
NF-kB p50-DBD:DNA co-crystal structure |
Muller et al.,
1995 |
RCSB PDB 1SVC |
GAL4-DBD:DNA co-crystal structure |
Hong et al.,
2008 |
RCSB PDB 3COQ |
PBX1-DBD:DNA co-crystal structure |
LaRonde-LeBlanc and Wolberger, 2003 |
RCSB PDB 1PUF |
UBX-DBD:DNA co-crystal structure |
Foos et al.,
2015 |
RCSB PDB 4UUS |
Raw gel images |
Mendeley |
https://doi.org/10.17632/5dnznn9kwt.1 |
Experimental Models: Cell
Lines |
Rosetta (DE3)pLysS Competent Cells |
Novagen |
Novagen # 70956–3 |
Experimental Models:
Organisms/Strains |
|
|
|
Oligonucleotides |
Table S3 |
|
|
Recombinant DNA |
GATCCTGTCTCCTGCTCTGTCAGCAGGGCACTGTACTTGCTGATACCAGGGAATGTTTGTTCTTAAATACCATCATTCCGGACGTGTTTGCCTTGGCCAGTTTTCCATGTACATGCAGAAAGAAGTTTGGACTGATCAATACAGTCCTCTGCCTTGGATC |
This paper |
160 bp ALBN1-DNA
|
GATCCATTACTTCTGAAACAGATGACTCCCAGCAGCTGCTGCCTGTGGCCCACAGGGCTTCCTGCCCTGCATGACAGCTGCACATCACATCCTGTGGTCATACTACTTCAGCCGCTTCTACGGCCAGATACAAAAGTGGGTGGGGAACATAGGCAAGGGATC |
This paper |
162 bp NRCAM-DNA
|
GATCCGCAGGGCCTCTCGGCTGCTGATCTTCAGCTGGTTGCTGAGAGTTGCAGCATTGCTGAGTCTTAGCAATGGATACTTCCCGATTCCCCTCACAAAAATAGGTCAGTCTGTCTGGCTAGTTCTGTACTTGCAGACACAGGGCATGTGGGGTTCCGGATC |
This paper |
162 bp CX3CR1-DNA
|
Software and Algorithms |
Gene Mapper v4.1 |
Thermo Fisher |
Cat no. 4440915 |
Peak Scanner module |
Thermo Fisher Scientific Cloud |
https://www.thermofisher.com/us/en/home/life-science/sequencing/fragment-analysis/fragment-analysis-fundamentals/fragment-analysis-software-data-analysis.html |
Pymol |
Schrodinger |
https://pymol.org/2/ |
PRISM 7 |
GraphPad |
https://www.graphpad.com/scientific-software/prism/ |
PROMO |
Messeguer et
al., 2002 |
http://alggen.lsi.upc.es/cgi-bin/promo_v3/promo/promoinit.cgi?dirDB=TF_8.3 |
GenePix Pro 7 |
Molecular Devices, LLC. |
http://mdc.custhelp.com/app/products/detail/p/129/~/version-7 |
R studio |
|
https://www.rstudio.com/ |
Fiji is Just ImageJ (Fiji) version
2.0.0-rc/1.51f |
|
https://imagej.net/ |
SWISS-MODEL |
Bienert et al.,
2017 |
https://swissmodel.expasy.org/ |
Other |
Human TF Protein microarrays |
Hu et al.,
2013 |
Human TF Protein microarrays |