Published datasets

Microarray

HaCaT keratinocytes
TGF-β3
(3 ng/ml, 1.5 h, 6 h, 24 h),
si-SMAD2/3, si-ETS1,
si-TFAP2A
GSE11710 Koinuma et al. (2009). Mol Cell Biol. 29, 172-86
TGF-β1(5 ng/ml, 24 h),
Ras(G12V), Ras(N116Y),
si-p53
GSE60814 Vasilaki et al. (2016). Sci Signal. 9, ra84
HepG2
TGF-β3(3 ng/ml, 1.5 h, 24 h),
si-HNF4α
GSE28798 Mizutani et al. (2011). J Biol Chem. 286, 29848-60
NCI-H441
TGF-β3(3 ng/ml, 1.5 h, 24 h),
si-TTF1
GSE51510 Isogaya et al. (2014). Cell Res. 24, 994-1008.
OCUM-2MLN
dnTβRII GSE12336 Komuro et al. (2009). J Natl Cancer Inst. 101, 592-604.
NMuMG, including Exon Array
TGF-β1(1 ng/ml, 24 h) GSE28184 Horiguchi et al. (2012). Oncogene 31, 3190-201.
Human umbilical vein endothelial cells (HUVEC)
BMP-6(50 ng/ml, 2 h, 24 h)
BMP-9(1 ng/ml, 2 h, 24 h)
GSE27661 Morikawa et al. (2011). Nucleic Acids Res. 39, 8712-8727.
BMP-9 (1 ng/ml, 24 h)
si-ATOH8 (LOF)

ATOH8 (GOF)
GSE104685 Morikawa et al. (2019). Sci Signal. 12, eaay4430.
Human pulmonary arterial smooth muscle cells (PASMC)
BMP-4(50 ng/ml, 2 h, 24 h) GSE27661 Morikawa et al. (2011). Nucleic Acids Res. 39, 8712-8727.

RNA-seq

HEK293T
si-ESRP2, si-Arkadia GSE60559 Mizutani et al. (2016). Oncogene 35, 3514-23.
A549 (Human lung adenocarcinoma)
TGF-β3(1 ng/ml, 1.5 h, 24 h),
Ad-TTF1
GSE51510 Isogaya et al. (2014). Cell Res. 24, 994-1008.
TGF-β3(2.5 ng/ml, 24 h),
sh-RBM47
GSE61910 Sakurai et al. (2016). Oncogene 35, 5000-5009.
si-TUFT1 GSE99149 Kawasaki et al. (2018). Cell Discov. 4, 1.
TGF-β3(1 ng/ml, 24 h),
sh-NORAD
GSE109296 Kawasaki et al. (2018). Cancer Sci. 109, 2211-2220.
NCI-H441 (Human lung adenocarcinoma)
si-TTF1 GSE129341 Hokari et al. (2020). Mol Oncol. 14, 277-293.
NCI-H209 (Human Lung small cell carcinoma)
si-TTF1, si-ASCL1 GSE129341 Hokari et al. (2020). Mol Oncol. 14, 277-293.
T47D (Human breast cancer cell line, classified as Luminal A)
Activin A(50 ng/ml, 24 h)
Palbociclib (CDK4/6 inhibitor)
GSE117502 Harada et al. (2019). Cancer Sci.. 110, 209-220.
MDA-MB-231-D (Human breast cancer cell line, classified as triple-negative)
TGF-β3(1 ng/ml, 24 h)
si-ZEB1, si-ZEB2
GSE89206 Katsura et al. (2017). Mol Oncol. 11, 1241-1262.
SUIT-2 (human pancreatic carcinoma)
Parental cells
and sublines
GSE107960 Takahashi et al. (2018). Oncogene 37, 2757-2772.
Panc-1 (human pancreatic carcinoma)
Parental cells
and sublines
GSE107960 Takahashi et al. (2018). Oncogene 37, 2757-2772.
HT-29 (Human colorectal adenocarcinoma)
LDN-193189 GSE96914 Yokoyama et al. (2017). Cancer Res. 77, 4026-4038.
DLD-1 (Human colorectal adenocarcinoma)
LDN-193189 GSE96914 Yokoyama et al. (2017). Cancer Res. 77, 4026-4038.
OS-RC-2 (Human renal cell carcinoma)
si-ESRP2, si-Arkadia GSE66741 Mizutani et al. (2016). Oncogene 35, 3514-3523.
Caki-1 (Human renal cell carcinoma)
TGF-β2(0.3 ng/ml, 24 h)
sh-TGFBR3
GSE106719 Nishida et al. (2018). Oncogene 37, 2197-2212.
Mouse pancreatic endothelial cell line, MS-1
TGF-β2(1 ng/ml, 72 h)
miRNA inhibitors
GSE70207 Katsura et al. (2016). Genes Cells. 21, 99-116.
EpH4/EpRas (normal mammary epithelial cells with/without oncogenic Ras)
TGF-β3(1 ng/ml, 48 h),
si-Etv4 and si-Etv5
GSE69387 Arase et al. (2017). Sci Rep. 7, 1166.
TGS-01 and TGS-04 (patient-derived glioma-initiating cell lines)
BMP-4(20 ng/ml, 24 h) JGAS00000000077 Raja et al. (2017). Oncogene 36, 4963-4974.
BMP-2 (100 ng/ml, 24 h),
EPHA6(WT), EPHA6(K757R)
JGAS00000000077 Raja et al. (2019). Cancer Sci.. 110, 3486-3496.
Mouse embryonic stem cells (mESCs)
LIF+BMP-4(10 ng/ml, 24 h) GSE70581 Morikawa et al. (2016). Stem Cell Reports 6, 64-73.

ChIP-chip, ChIP-seq

HaCaT keratinocytes
SMAD2/3 ChIP-chip GSE11710 Koinuma et al. (2009). Mol Cell Biol. 29, 172-86
LacZ, p63 ChIP-seq
TGF-β1/LacZ, p63 ChIP-seq
TGF-β1/Ras(G12V), p63 ChIP-seq
TGF-β1/Ras(N116Y), p63 ChIP-seq
GSE60814 Vasilaki et al. (2016) Sci Signal. 9, ra84
HepG2
SMAD2/3 ChIP-chip
HNF4α ChIP-seq
GSE28798 Mizutani et al. (2011). J Biol Chem. 286, 29848-60
Hep3B
SMAD2/3 ChIP-chip GSE28798 Mizutani et al. (2011). J Biol Chem. 286, 29848-60
A549 (Human lung adenocarcinoma)
TGF-β3, SMAD3 ChIP-seq GSE51510 Isogaya et al. (2014). Cell Res. 24, 994-1008.
NCI-H441 (Human lung adenocarcinoma)
TGF-β3/siCtrl, SMAD3 ChIP-seq
TGF-β3/siTTF1, SMAD3 ChIP-seq
TGF-β3/siCtrl, SMAD4 ChIP-seq
TGF-β3/siTTF1, SMAD4 ChIP-seq
TTF1 ChIP-seq
TGF-β3, TTF1 ChIP-seq
GSE51510 Isogaya et al. (2014). Cell Res. 24, 994-1008.
TTF-1 ChIP-seq, rep2
ASCL1 ChIP-seq, rep1
ASCL1 ChIP-seq, rep2
GSE129341 Hokari et al. (2020). Mol Oncol. 14, 277-293.
NCI-H209 (Human Lung small cell carcinoma)
TTF-1 ChIP-seq, rep1
TTF-1 ChIP-seq, rep2
ASCL1 ChIP-seq, rep1
ASCL1 ChIP-seq, rep2
GSE129341 Hokari et al. (2020). Mol Oncol. 14, 277-293.
NCI-H345-TbRII
SMAD2/3 ChIP-seq** GSE63871 Murai et al. (2015). Cell Discov. 1, 15026.
MDA-231-D (Human breast cancer cell line, classified as triple-negative)
ZEB1 ChIP-seq** GSE89206 Katsura et al. (2017). Mol Oncol. 11, 1241-1262.
Hs-578-T (Human breast cancer cell line, classified as triple-negative)
Activin A, SMAD2 ChIP-seq, rep1
Activin A, SMAD2 ChIP-seq, rep2
Activin A/Palbociclib, SMAD2 ChIP-seq, rep1
Activin A/Palbociclib, SMAD2 ChIP-seq, rep2
GSE117502 Harada et al. (2019). Cancer Sci. 110, 209-220.
ZEB1 ChIP-seq** GSE89206 Katsura et al. (2017). Mol Oncol. 11, 1241-1262.
MCF7 (Human breast cancer cell line, classified as Luminal A)
ZEB1 ChIP-seq** GSE89206 Katsura et al. (2017). Mol Oncol. 11, 1241-1262.
T47D (Human breast cancer cell line, classified as Luminal A)
Activin A, SMAD2 ChIP-seq, rep1
Activin A, SMAD2 ChIP-seq, rep2
Activin A/Palbociclib, SMAD2 ChIP-seq, rep1
Activin A/Palbociclib, SMAD2 ChIP-seq, rep2
GSE117502 Harada et al. (2019). Cancer Sci. 110, 209-220.
EpH4/EpRas (normal mammary epithelial cells with/without oncogenic Ras)
Etv4 ChIP-seq
Etv5 ChIP-seq
GSE69387 Arase et al. (2017). Sci Rep. 7, 1166.
Human umbilical vein endothelial cells (HUVECs)
BMP-6, SMAD1/5 ChIP-seq
BMP-9, SMAD1/5 ChIP-seq
GSE27661 Morikawa et al. (2011). Nucleic Acids Res. 39, 8712-8727.
Human pulmonary arterial endothelial cells (HPAECs)
BMP-9, SMAD1/5 ChIP-seq, rep1
BMP-9, SMAD1/5 ChIP-seq, rep2
FLAG-ATOH8 ChIP-seq, rep1
FLAG-ATOH8 ChIP-seq, rep2
GSE104685 Morikawa et al. (2019). Sci Signal. 12, eaay4430.
Human pulmonary arterial smooth muscle cells (PASMCs)
BMP-4, SMAD1/5 ChIP-seq GSE27661 Morikawa et al. (2011). Nucleic Acids Res. 39, 8712-8727.
Mouse embryonic stem cells (mESCs)
naive/serum, Smad1/5 ChIP-seq
naive/BMP-4, Smad1/5 ChIP-seq
primed/BMP-4 1.5h, Smad1/5 ChIP-seq
primed/BMP-4 24h, Smad1/5 ChIP-seq
GSE70581 Morikawa et al. (2016). Stem Cell Reports 6, 64-73.
* ChIP-seq data were re-analyzed and mapped to the latest version of the genome (hg38 or mm10).
** Peaks were called with the ChIP data alone, without control sample(s).

FAIRE-seq

EpH4/EpRas (normal mammary epithelial cells with/without oncogenic Ras)
TGF-β3
(1 ng/ml, 4 or 8 d),
si-Etv4 and si-Etv5
GSE69387 Arase et al. (2017). Sci Rep. 7, 1166.