SMAD Binding Resource | Masato Morikawa

ChIP-chip, ChIP-seq, CUT&Tag, CUT&RUN

UCSC Genome Browser links are shown for entries with reprocessed bigWig tracks.

HaCaT keratinocytes
SMAD2/3 ChIP-chip, TGF-β3, 1.5 h	GSE11710	Koinuma et al, Mol Cell Biol, 2009, doi: 10.1128/MCB.01038-08
SMAD2 ChIP-seq, TGF-β3, 1.5 h, rep1 SMAD2 ChIP-seq, TGF-β3, 1.5 h, rep2 SMAD3 ChIP-seq, TGF-β3, 1.5 h, rep1 SMAD3 ChIP-seq, TGF-β3, 1.5 h, rep2	GSE180252	Ogami et al, J Biochem, 2022, doi: 10.1093/jb/mvab141
p63 ChIP-seq, LacZ p63 ChIP-seq, TGF-β3, 1.5 h/LacZ p63 ChIP-seq, TGF-β3, 1.5 h/Ras(G12V) p63 ChIP-seq, TGF-β3, 1.5 h/Ras(N116Y)	GSE60814	Vasilaki et al, Sci Signal, 2016, doi: 10.1126/scisignal.aag3232
Differentiated human progenitor epidermal keratinocytes (HPEK)
SMAD3 ChIP-seq, TGF-β3, 1.5 h	GSE180252	Ogami et al, J Biochem, 2022, doi: 10.1093/jb/mvab141
HepG2
SMAD2/3 ChIP-chip, TGF-β3, 1.5 h	GSE28798	Mizutani et al, J Biol Chem, 2011, doi: 10.1074/jbc.M110.217745
Hep3B
SMAD2/3 ChIP-chip, TGF-β3, 1.5 h	GSE28798	Mizutani et al, J Biol Chem, 2011, doi: 10.1074/jbc.M110.217745
Human intestinal organoids
SMAD3 CUT&RUN, APC-KO/ARID1A-KO SMAD3 CUT&RUN, APC-KO/ARID1A-KO, TGF-β1, 30 min SMAD3 CUT&RUN, APC-KO/SMARCA4-KO SMAD3 CUT&RUN, APC-KO/SMARCA4-KO, TGF-β1, 30 min SMAD3 CUT&RUN, APC-KO SMAD3 CUT&RUN, APC-KO, TGF-β1, 30 min	GSE145183	Ringel et al, Cell Stem Cell, 2020, doi: 10.1016/j.stem.2020.02.007
MCF10A MII (Human breast epithelial cell line)
SMAD2/3 ChIP-seq, TGF-β3, 1.5 h SMAD2/3 ChIP-seq, TGF-β3, 16 h	GSE83787	Sundqvist et al, Nucleic Acids Res, 2018, doi: 10.1093/nar/gkx1190
Hs578T (Human breast cancer cell line, classified as triple-negative)
SMAD2/3 ChIP-seq, TGF-β3, 1.5 h SMAD2/3 ChIP-seq, TGF-β3, 16 h	GSE104352	Sundqvist et al, Nucleic Acids Res, 2018, doi: 10.1093/nar/gkx1190
SMAD2 ChIP-seq, Activin A, 1.5 h, rep1 SMAD2 ChIP-seq, Activin A, 1.5 h, rep2 SMAD2 ChIP-seq, Activin A, 1.5 h/Palbociclib, rep1 SMAD2 ChIP-seq, Activin A, 1.5 h/Palbociclib, rep2	GSE117502	Harada et al, Cancer Sci, 2019, doi: 10.1111/cas.13841
BT549 (Human breast cancer cell line, classified as triple-negative)
SMAD2/3 ChIP-seq, TGF-β3, 1.5 h SMAD2/3 ChIP-seq, TGF-β3, 16 h	GSE104352	Sundqvist et al, Nucleic Acids Res, 2018, doi: 10.1093/nar/gkx1190
T47D (Human breast cancer cell line, classified as Luminal A)
SMAD2 ChIP-seq, Activin A, 1.5 h, rep1 SMAD2 ChIP-seq, Activin A, 1.5 h, rep2 SMAD2 ChIP-seq, Activin A, 1.5 h/Palbociclib, rep1 SMAD2 ChIP-seq, Activin A, 1.5 h/Palbociclib, rep2	GSE117502	Harada et al, Cancer Sci, 2019, doi: 10.1111/cas.13841
A549 (Human lung adenocarcinoma)
SMAD3 ChIP-seq, TGF-β3, 1.5h	GSE51510	Isogaya et al, Cell Res, 2014, doi: 10.1038/cr.2014.97
NCI-H441 (Human lung adenocarcinoma)
SMAD3 ChIP-seq, TGF-β3, 1.5 h/siCtrl SMAD3 ChIP-seq, TGF-β3, 1.5 h/siTTF1 SMAD4 ChIP-seq, TGF-β3, 1.5 h/siCtrl SMAD4 ChIP-seq, TGF-β3, 1.5 h/siTTF1 TTF1 ChIP-seq TTF1 ChIP-seq, TGF-β3, 1.5 h	GSE51510	Isogaya et al, Cell Res, 2014, doi: 10.1038/cr.2014.97
NCI-H345-TbRII
SMAD2/3 ChIP-seq^*	GSE63871	Murai et al, Cell Discov, 2015, doi: 10.1038/celldisc.2015.26
Human umbilical vein endothelial cells (HUVECs)
SMAD1/5 ChIP-seq, BMP-6, 1.5 h SMAD1/5 ChIP-seq, BMP-9, 1.5 h	GSE27661	Morikawa et al, Nucleic Acids Res, 2011, doi: 10.1093/nar/gkr572
Human pulmonary arterial endothelial cells (HPAECs)
SMAD1/5 ChIP-seq, BMP-9, 1.5 h, rep1 SMAD1/5 ChIP-seq, BMP-9, 1.5 h, rep2 FLAG-ATOH8 ChIP-seq, rep1 FLAG-ATOH8 ChIP-seq, rep2	GSE104685	Morikawa et al, Sci Signal, 2019, doi: 10.1126/scisignal.aay4430
Human pulmonary arterial smooth muscle cells (PASMCs)
SMAD1/5 ChIP-seq, BMP-4, 1.5 h	GSE27661	Morikawa et al, Nucleic Acids Res, 2011, doi: 10.1093/nar/gkr572
C2C12 myotube
SMAD3 ChIP-seq, TGF-β1, 2 h, rep1 SMAD3 ChIP-seq, TGF-β1, 2 h, rep2	GSE21614	Mullen et al, Cell, 2011, doi: 10.1016/j.cell.2011.08.050
Mouse molar tooth germ (dental mesenchyme)
pSMAD1/5 CUT&RUN, dental mesenchyme, rep1 pSMAD1/5 CUT&RUN, dental mesenchyme, rep2 pSMAD3 CUT&RUN, dental mesenchyme, rep1 pSMAD3 CUT&RUN, dental mesenchyme, rep2	GSE297033	Tang et al, Development, 2025, doi: 10.1242/dev.204563
Human embryonic stem cells (hESCs)
SMAD2/3 ChIP-seq, Ab1 SMAD2/3 ChIP-seq, Ab2 SMAD3 ChIP-seq	GSE29422	Kim et al, Dev Biol, 2011, doi: 10.1016/j.ydbio.2011.06.009
Mouse embryonic stem cells (mESCs)
SMAD1/5 ChIP-seq, naive mESC /serum SMAD1/5 ChIP-seq, naive mESC /BMP-4 SMAD1/5 ChIP-seq, primed EpiLC/BMP-4, 1.5 h SMAD1/5 ChIP-seq, primed EpiLC/BMP-4, 24 h	GSE70581	Morikawa et al, Stem Cell Reports, 2016, doi: 10.1016/j.stemcr.2015.12.004
KDM1A ChIP-seq, mESC , rep1 KDM1A ChIP-seq, mESC , rep2 KDM1A ChIP-seq, SMAD1/5-dKO mESC , rep1 KDM1A ChIP-seq, SMAD1/5-dKO mESC , rep2	GSE268911	Morikawa et al, J Biol Chem, 2025, doi: 10.1016/j.jbc.2025.110591
SMAD2/3 ChIP-seq, mESC	GSE60286	Yoon et al, Nat Commun, 2015, doi: 10.1038/ncomms7546
SMAD2/3 ChIP-seq, EB day 3	GSE118765	Su et al, Nature, 2020, doi: 10.1038/s41586-019-1897-5
SMAD2/3 ChIP-seq, SMAD4-KO mESC SMAD2/3 ChIP-seq, SMAD4-KO EB, SB431542 SMAD2/3 ChIP-seq, SMAD4-KO EB + Activin A 2 h SMAD2/3 CUT&Tag, SMAD4-KO EB + Activin A SMAD2/3 CUT&Tag, SMAD4-KO/Dnmt3b-KD EB + Activin A SMAD2/3 CUT&Tag, WT mesendoderm + Activin A SMAD2/3 CUT&Tag, SMAD4-KO mesendoderm + Activin A	GSE240786 / GSE240787	Zhao et al, Nat Commun, 2024, doi: 10.1038/s41467-024-54433-5

Public ChIP-seq, CUT&RUN, and CUT&Tag datasets were reprocessed.
Reads were downloaded with prefetch, converted with fasterq-dump, and aligned to hg38 or mm10 with Bowtie2.
BAM files were sorted, indexed, deduplicated, and filtered with SAMtools.
CPM-normalized bigWig files were generated with bamCoverage after blacklist filtering.
Peaks were called with MACS3 at q = 0.01, using matched controls when available.
Peak and fold-enrichment tracks were further processed with BEDTools and UCSC bedGraphToBigWig.

^* Peaks were called with the ChIP data alone, without control sample(s).

Microarray

Expression datasets related to the signaling conditions and downstream responses shown above.

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, Mol Cell Biol, 2009, doi: 10.1128/MCB.01038-08
TGF-β1 (5 ng/ml, 24 h) Ras(G12V), Ras(N116Y), si-p53	GSE60814	Vasilaki et al, Sci Signal, 2016, doi: 10.1126/scisignal.aag3232
HepG2
TGF-β3 (3 ng/ml, 1.5 h, 24 h) si-HNF4α	GSE28798	Mizutani et al, J Biol Chem, 2011, doi: 10.1074/jbc.M110.217745
NCI-H441
TGF-β3 (3 ng/ml, 1.5 h, 24 h) si-TTF1	GSE51510	Isogaya et al, Cell Res, 2014, doi: 10.1038/cr.2014.97
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, Nucleic Acids Res, 2011, doi: 10.1093/nar/gkr572
Human pulmonary arterial smooth muscle cells (PASMC)
BMP-4 (50 ng/ml, 2 h, 24 h)	GSE27661	Morikawa et al, Nucleic Acids Res, 2011, doi: 10.1093/nar/gkr572
C2C12 myotube
TGF-β1 (2.5 ng/ml, 12 h)	GSE21608	Mullen et al, Cell, 2011, doi: 10.1016/j.cell.2011.08.050

RNA-seq

Selected transcriptome datasets matched or related to the binding datasets shown above.

Human progenitor epidermal keratinocytes (HPEK)
TGF-β3 (1 ng/ml, 24 h) differentiated and undifferentiated HPEK cells	GSE180251	Ogami et al, J Biochem, 2022, doi: 10.1093/jb/mvab141
Human intestinal organoids
TGF-β1 (10 ng/ml, 24 h) without A83-01 APC-KO, APC-KO/ARID1A-KO, APC-KO/SMARCA4-KO	GSE145308	Ringel et al, Cell Stem Cell, 2020, doi: 10.1016/j.stem.2020.02.007
MCF10A MII (Human breast epithelial cell line)
TGF-β3 (5 ng/ml, 1.5 h, 16 h) si-JUNB	GSE83786	Sundqvist et al, Nucleic Acids Res, 2018, doi: 10.1093/nar/gkx1190
A549 (Human lung adenocarcinoma)
TGF-β3 (1 ng/ml, 24 h) Ad-LacZ, Ad-TTF1	GSE51510	Isogaya et al, Cell Res, 2014, doi: 10.1038/cr.2014.97
NCI-H441 (Human lung adenocarcinoma)
TGF-β3 (3 ng/ml, 1.5 h, 24 h) si-TTF1	GSE51510	Isogaya et al, Cell Res, 2014, doi: 10.1038/cr.2014.97
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, Cancer Sci, 2019, doi: 10.1111/cas.13841
Mouse molar tooth germ (dental mesenchyme)
SB431542, SIS3 (pSMAD3 inhibitor)	GSE297137	Tang et al, Development, 2025, doi: 10.1242/dev.204563
Mouse embryonic stem cells (mESCs)
LIF+serum, LIF+BMP-4 (10 ng/ml)	GSE70581	Morikawa et al, Stem Cell Reports, 2016, doi: 10.1016/j.stemcr.2015.12.004