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). |