Development143:doi:10.1242/dev.130898:Supplementaryinformation
Supplementary Materials and Methods
In situ hybridization probes
In situ hybridization was carried out using the following mouse cDNA probe templates: pSport1-Fn1-31-38
(nt +4891 - +6157), pCMV-Sport6-Cd74 (IMAGE ID 2650401), pBSK-Prokr2-II (nt -275 - +741), pBSKNrp2-II (nt +1147 - +3503), pBSK-Gli1 and pBSK-Sox9 (kindly provided by T. Willnow), pCMV-Sport6.1Frem1 (IMAGE ID 6510171), pCMV-Sport6.1-Mmp9 (IMAGE ID 6309245), pCMV- Sport6-Etv4 (IMAGE
ID 4021693), pYX-Asc-Scube1 (IMAGE ID 6850999), pFLCI-Madcam1 (FANTOM Full Length cDNA
clone 9430044H04), pGEM-Foxi3 (nt 3851 – 4461, GeneID: 232077), pGEM-Ascl4 (nt -180 – +785,
GeneID:67341), pCR-BluntII-TOPO-Tnc (IMAGE ID 40099596), pCMV- Sport6-Pthlh (IMAGE ID
3594509), pYX-Asc-Tnfaip3 (IMAGE ID 6838303), pCR-BluntII-TOPO-Tsku (IMAGE-ID 40095311),
pGEM-Ctgf (kindly provided by M. Mikkola), Bmp2 and Ptch1 (kindly provided by J. Huelsken).
qRT-PCR primers
Reference genes :
mActb_RT_fwd sense:
mActb_RT_rev antisense:
mGapdh_RT_fwd2 sense:
mGapdh_RT_rev2 antisense:
mHmbs_RT_fwd sense:
mHmbs_RT_rev antisense:
5´ TTACTGCTCTGGCTCCTAG 3´
5´ CTCATCGTACTCCTGCTTG 3´
5´TGTGAACCACGAGAAATATGAC 3´
5´ GTGATGGCATGGACTGTG 3´
5´ CTGAAAGCCTTGTACCCTG 3´
5´ GCGTTTTCTAGCTCCTTGG 3´
Target genes:
mAscl4_RT_fwd2 sense:
mAscl4_RT_rev2 antisense:
mBmp2_RT_fwd sense:
mBmp2_RT_rev antisense:
mBmp4_RT_fwd2 sense
mBmp4_RT_rev2 antisense
mCd74_RT_fwd sense:
mCd74_RT_rev antisense:
mCol1a1_RT_fwd1 sense
mCoL1a1_RT_rev1 antisense
mCtgf_RT_fwd sense:
mCtgf_RT_rev antisense:
mDkk4_RT_fwd sense:
mDkk4_RT_rev antisense:
mEdaR_RT_fwd2 sense:
mEdaR_RT_rev2 antisense:
mEtv4_RT_fwd sense:
mEtv4_RT_rev antisense:
mEtv5_RT_fwd2 sense:
mEtv5_RT_rev2 antisense:
mFn1_RT_fwd sense:
mFn1_RT_rev antisense:
mFoxi3_RT_fwd sense:
mFoxi3_RT_rev2 antisense:
mFrem1_RT_fwd sense:
mFrem1_RT_rev antisense:
mGli1_RT_fwd2 sense:
mGli1_RT_rev2 antisense:
mIrx1_RT_fwd1 sense
mIrx1_RT_rev1 antisense
mItgb8_RT_fwd sense:
5´ TAGCAGCATCCTAGCCCACT 3´
5´ ACTCGGAACCAATGAAGGTG 3´
5´ GCAGCTTCCATCACGAA 3´
5´ TTCCTGTATCTGTTCCCG 3´
5´ GTAGTGCCATTCGGAGCG 3´
5´ ATCAGCATTCGGTTACCAGG 3´
5´ GAAATCTGCCAAACCTGTG 3´
5´ GGTCATGTTGCCGTACTT 3´
5´ CTGCACGAGTCACACCGGAA 3´
5´ GGGAGGGAACCAGATTGGGG 3´
5´ CCACCCGAGTTACCAATG 3´
5´ TGGCGATTTTAGGTGTCC 3´
5´ AGCAGAGGAAAACAGACC 3´
5´ CCACAGTCAGAGGTTCTAAG 3´
5´ GGATGTGTATGCCAACGTG 3´
5´ GCCATGTTTTCACGACCG 3´
5´ ACCTCAGTCACTTCCAAGAG 3´
5´ GTTCCTTCTTGATCCTGGTG 3´
5´ GCAGTTTGTCCCAGATTTTCA 3´
5´ GGCACTTTTCTCCATACTTAGC 3´
5´GGAGAACAAAGACAGAGACAA 3´
5´ GGTGGATCTTGTAGTCAGTG 3´
5´ AACTCCATCCGCCACAAC 3´
5´ CTTCCCACTCACTCTTAGTC 3´
5´ ACCAGTTCACAGTATATGCC 3´
5´ CCAGTTCTACCATGTGCC 3´
5´ TCAATCCAATGACTCCACC 3´
5´ GGACCCTGACATAAAGTTG 3´
5´ ACCCAACTACAGCGCCTTCTT 3´
5´ TCATACTGAGAGCCCATCTGCG 3´
5´ GCAGCCTGGGTATTTTCAC 3´
Development • Supplementary information
mItgb8_RT_rev antisense:
mLhx2_RT_fwd sense:
mLhx2_RT_rev antisense:
mMadcam1_RT_fwd3 sense:
mMadcam1_RT_rev3 antisense:
mMmp9_RT_fwd sense:
mMmp9_RT_rev antisense:
mNcam1_RT_fwd sense:
mNcam1_RT_rev antisense:
mNgfr_RT_fwd1 sense
mNgfr_RT_rev1 antisense
mNrp1_RT_fwd sense:
mNrp1_RT_rev antisense:
mNrp2_RT_fwd sense:
mNrp2_RT_rev antisense:
mProkr2_RT_fwd sense:
mProkr2_RT_rev2 antisense:
mPthlh_RT_fwd sense:
mPthlh_RT_rev antisense:
mPtch1_RT_fwd sense:
mPtch1_RT_rev antisense:
mPtch2_RT_fwd2 sense:
mPtch2_RT_rev2 antisense:
mRelb_RT_fwd2 sense:
mRelb_RT_rev2 antisense:
mScube1_RT_fwd2 sense:
mScube1_RT_rev2 antisense:
mSfrp1_RT_fwd sense:
mSfrp1_RT_rev antisense:
mShh_RT_fwd sense:
mShh_RT_rev antisense:
mSox9_RT_fwd2 sense:
mSox9_RT_rev2 antisense:
mSox21_RT_fwd sense:
mSox21_RT_rev antisense:
mTnc_RT_fwd sense:
mTnc_RT_rev antisense:
mTnfaip3_RT_fwd2 sense:
mTnfaip3_RT_rev2 antisense:
mTrps1_RT_fwd sense:
mTrps1_RT_rev antisense:
mTsku_RT_fwd sense:
mTsku_RT_rev antisense:
mTspan18_RT_fwd2 sense:
mTspan18_RT_rev2 antisense:
mWif1_RT_fwd sense:
mWif1_RT_rev antisense:
5´ GCACAGGAGACCACATTTG 3´
5´ GCAGCCAAAAGACAAAGCG 3´
5´ GTAAAAGGTTGCGCCTGAAC 3´
5´ CCAATCTGTATGTTCCTGGC 3´
5´ TCTCTGCCTCCTTTAGTCTG 3´
5´ GGACAGCCAGACACTAAAG 3´
5´ CGGCAAGTCTTCAGAGTAG 3´
5´ CCCACAGGAGTTTAAGGAAG 3´
5´ GGACAGGACTATGAACCG 3´
5´ GCCTGGACAGTGTTACGTTCTC 3´
5´ CGGACATACTCTGCAGGCCC 3´
5´ TCCGAATCAAACCTGTATCCTG 3´
5´GATGCTGTAATCTGGGAGTCTG 3´
5´ TTCCTGACCTTTGACCTG 3´
5´ GGAGTTTGGAGGGTGTTT 3´
5´ CTCCGTCAACTACCTTCGTAC 3´
5´ GACCAAAGCGATCAGGAAGG 3´
5´ GGAGTGTCCTGGTATTCCTG 3´
5´ ACTTGCCCTTGTCATGC 3´
5´ GGTCCTCGCTTACAAACTC 3´
5´ CGGTCAGGTAGATGTAGAAAG 3´
5´ GCTTACTTCCAAGGTCTACTC 3´
5´ AGTCTGAATCAACATCTGGG 3´
5´ GCTGTACTTGCTCTGTGAC 3´
5´ GGTGGCGTTTTGAACAC 3´
5´ CCTTGCCCAAAACCAGAAG 3´
5´ GACCATCTGCATGTAAGGC 3´
5´ CGGAAGCCTCTAAGCCC 3´
5´ TCTTGTCACCGTTTTCCTTC 3´
5´ GGCAGATATGAAGGGAAGATC 3´
5´ CATTTAACTTGTCTTTGCACC 3´
5´ GCAAGACTCTGGGCAAG 3´
5´ GCTGGTACTTGTAATCGGG 3´
5´ TGGTGTTTGCTTTGCACTTC 3´
5´ GGAGGGAGGAAGGATGAGAC 3´
5´ GAGGACTTCTATCGCAACTGG 3´
5´ CTTGGGCTGTGATTTTGCTC 3´
5´GGAAACAGGACTTTGCTACG3´
5´GATGTTGCTGAGGACAAATATG3´
5´ GCCATTCCAAAGACTTCCAG 3´
5´ AGTTTTCCGTCCAATGCC 3´
5´ GCTCCCCCTTGAGTGACATC 3´
5´ GGAAGCAGGCGATGGATAAG 3´
5´ CTTACCAAGCACTACCAAGG 3´
5´ TCAGTGTCCAGCGTCAG 3´
5´ CCACTCCATGAATTTTACCTG 3´
5´ AGGGACATTGACAGTTGG 3´
Chromatin immunoprecipitation primers
Reference region:
mGapdh-ChIP-TSS-fwd sense:
mGapdh-ChIP-TSS-rev2 antisense:
5´ GCCTGAGCTAGGACTGG 3´
5´ AGGGCTGCAGTCCGTATTTA 3´
NF-κB binding sites:
mLhx2-ChIP-+14550-fwd2 sense:
mLhx2-ChIP-+14550-rev antisense:
mSox9-ChIP-+2903-fwd2 sense:
5´ CATCCTGATTCCCTTCTGGA 3´
5´ GGGCTGACTTTCTGCACTTT 3´
5´ CATTGCTGGAGGGAGAAAAG 3´
Development • Supplementary information
Development143:doi:10.1242/dev.130898:Supplementaryinformation
Development143:doi:10.1242/dev.130898:Supplementaryinformation
5´ GCCTAGAGGTGGATGGATGA 3´
5´ TGTTGCAGACCTAAGAAGGACA 3´
5´ CAACCTCACATGCCACACTT 3´
5´ TCTTTCCTTCCCCAAGGAGT 3´
5´ CCATCCCCACACTGTAGGTT 3´
Development • Supplementary information
mSox9-ChIP-+2903-rev2 antisense:
mTrps1-ChIP--62449-fwd sense:
mTrps1-ChIP--62449-rev antisense:
mMmp9-ChIP-+46fwd sense:
mMmp9-ChIP-+46rev antisense:
Development143:doi:10.1242/dev.130898:Supplementaryinformation
Fig. S1. Isolation of primary placode keratinocytes using NF-κB-specific EGFP reporter mice (κEGFP). (A) EGFP expression pattern in κ-EGFP, κ-EGFP;tabby and κ-EGFP;∆N embryos at E14.5.
(B) Enzymatically and mechanically separated epidermal keratinocytes from κ-EGFP embryos (n =
5) were sorted via FACS into an EGFP-positive (primary placode-specifc, P2) and EGFP-negative
(interfollicular keratinocytes, P1) cell population. Purity of both populations was determined over a
resort, in which both populations showed a recovery rate of over 95%. Purified cell populations
Development • Supplementary information
were used for microarray analysis, qRT-PCR and ChIP experiments.
Fig. S2. Dermal markers were absent in epidermal keratinocyte samples of N, Lhx2-KOs and of
corresponding controls. (A,B) Quantitative real-time PCR (qRT-PCR) analysis f o r B m p 4 ,
C o l 1 a 1 , I r x 1 a n d N g f r e x p r e s s i o n using either RNA samples from epidermal keratinocytes of
n = 3 ∆N (A), Lhx2-KO (B) and corresponding control embryos at E14.5. Statistical analyses were
performed using a two-tailed unpaired t-test. Data are presented as mean±s.e.m.
Development • Supplementary information
Development143:doi:10.1242/dev.130898:Supplementaryinformation
Fig. S3. Verification of placode-specific expression and of NF-κB dependence of selected genes
from microarray analysis. (A,B) Quantitative real-time PCR (qRT-PCR) analysis using either RNA
samples from epidermal keratinocytes of
n = 3 controls or ∆N embryos (A), or RNA samples
isolated from EGFP- positive (placode) or EGFP-negative (IFE) sorted keratinocytes (B) at E14.5.
Statistical analyses were performed using a two-tailed unpaired t-test. Data are presented as
mean±s.e.m. * P<0.05; ** P<0.01; *** P<0.001. (C) In situ hybridization for mRNAs of NF-κB
target genes using representative sagittal sections of n = 3 ∆N and control embryos at E14.5.
Dashed lines indicate boundary between epidermis and dermis. Scale bars: 50 µm.
Development • Supplementary information
Development143:doi:10.1242/dev.130898:Supplementaryinformation
Development143:doi:10.1242/dev.130898:Supplementaryinformation
Fig. S4. Treatment of embryonic control skin explants with recombinant TGFβ2 slightly
enhanced primary HF induction. (A) Embryonic skin explants from n = 3 E14.5 control and ∆N
embryos were either left untreated (Control) or treated with recombinant TGFβ2 (100 ng/ml) for 24
hrs. n = 1 8 samples o f e a c h e x p e r i m e n t a l g r o u p were stained with H&E and follicles
were quantified in numbers of hair follicle placodes/microscopic field in relation to the control
group. Scale bars: 100µm. (B) Immunostaining on TGF-β2-stimulated embryonic control skin
sections corresponding to E15.5 using antibodies against pFAK, Ki67 and E-Cadherin, as well as
against EDAR and KRT14 to indicate placodes. Scale bars: 20 µm / 50 µm (pSMAD2). Arrowheads
Development • Supplementary information
indicate pFAK expression in HF placodes; dashed lines delineate dermal-epidermal boundaries.
Development 143: doi:10.1242/dev.130898: Supplementary information
Supplementary Table S1. Representative lists of genes enriched in E14.5 primary hair follicle placodes
(upper list) or in the interfollicular epidermis (IFE; lower list). Only mRNAs differentially regulated ≥
1.5x in hair follicle placodes vs. IFE are listed. Hair follicle placode keratinocytes correspond to
EGFP-expressing and IFE keratinocytes to EGFP-non-expressing cells separated by FACS (see main text
and Fig. S1).
Genes symbol
Frem1
Dkk4
Fn1
Ascl4
Slc14a1
Trps1
Prokr2
Foxi3
Nrp2
Wif1
Tspan18
Socs2
Ltb
Cd74
Tgfb2
Necab1
Fgf20
Dusp6
Tmem100
Edar
Rragd
Itgb8
Tll1
Mical2
Steap4
Adamts3
Has3
Fgd5
Tnf
Etv4
Description
Ref_Seq
Fras1 related extracellular matrix protein 1
dickkopf homolog 4 (Xenopus laevis)
fibronectin 1
achaete-scute complex homolog 4 (Drosophila)
solute carrier family 14 (urea transporter),
member 1
trichorhinophalangeal syndrome I (human)
prokineticin receptor 2
forkhead box I3
neuropilin 2
Wnt inhibitory factor 1
tetraspanin 18
suppressor of cytokine signaling 2
lymphotoxin B
CD74 antigen
transforming growth factor, beta 2
N-terminal EF-hand calcium binding protein 1
fibroblast growth factor 20
dual specificity phosphatase 6
transmembrane protein 100
ectodysplasin-A receptor
Ras-related GTP binding D
integrin beta 8
tolloid-like
microtubule associated monoxygenase,
calponin and LIM domain containing 2
NM_177863
NM_145592
NM_010233
NM_001163614
NM_001171010
Fold
change
6.72678
5.82304
5.04024
4.84369
4.59977
NM_032000
NM_144944
NM_001101464
NM_001077403
NM_011915
NM_183180
NM_007706
NM_008518
NM_001042605
NM_009367
NM_178617
NM_030610
NM_026268
NM_026433
NM_010100
NM_027491
NM_177290
NM_009390
NM_177282
4.32476
4.31001
4.23003
4.15898
4.10489
4.02829
3.96253
3.72502
3.448
3.40851
3.33139
3.29271
3.21706
3.17391
3.15788
3.11128
3.08216
3.07956
3.06069
STEAP family member 4
a disintegrin-like and metallopeptidase with
thrombospondin motifs 3
hyaluronan synthase 3
FYVE, RhoGEF and PH domain containing 5
tumor necrosis factor
ets variant gene 4 (E1A enhancer binding
protein, E1AF)
NM_054098
NM_177872
3.0561
2.97619
NM_008217
NM_172731
NM_013693
NM_008815
2.95032
2.88688
2.83063
2.82086
Development • Supplementary information
Genes enriched in primary hair follicle placodes at E14.5:
Nkain3
Shh
Prss35
Ifitm1
Lgr6
Aff2
Clip3
C1s
Ncam1
Madcam1
Cntnap1
Rasgef1b
Myb
Moxd1
Tnfaip3
Csgalnact1
Mapk4
Stra6
Krt17
Kcnmb4
Mmp9
Srgap1
Ctgf
Stxbp6
Lass4
Scube1
Cpe
Pthlh
Alox12e
Ptch2
Scd1
Dchs1
Cyfip2
Rhpn2
Prnd
Cxcr4
Cxcl9
Setbp1
Lgi2
Na+/K+ transporting ATPase interacting 3
sonic hedgehog
protease, serine, 35
interferon induced transmembrane protein 1
leucine-rich repeat-containing G proteincoupled receptor 6
AF4/FMR2 family, member 2
CAP-GLY domain containing linker protein 3
complement component 1, s subcomponent
neural cell adhesion molecule 1
mucosal vascular addressin cell adhesion
molecule 1
contactin associated protein-like 1
RasGEF domain family, member 1B
myeloblastosis oncogene
monooxygenase, DBH-like 1
tumor necrosis factor, alpha-induced protein 3
chondroitin sulfate Nacetylgalactosaminyltransferase 1
mitogen-activated protein kinase 4
stimulated by retinoic acid gene 6
keratin 17
potassium large conductance calcium-activated
channel, subfamily M beta member 4
NM_172987
NM_009170
NM_178738
NM_026820
NM_001033409
2.77675
2.76033
2.71064
2.7034
2.67464
NM_008032
NM_001081114
NM_144938
NM_001081445
NM_013591
2.67125
2.66474
2.63794
2.63623
2.63337
NM_016782
NM_145839
NM_010848
NM_021509
NM_009397
NM_172753
2.62987
2.60963
2.59304
2.59
2.58453
2.58372
NM_172632
NM_009291
NM_010663
NM_021452
2.5564
2.55396
2.55127
2.53788
matrix metallopeptidase 9
SLIT-ROBO Rho GTPase activating protein 1
connective tissue growth factor
syntaxin binding protein 6 (amisyn)
LAG1 homolog, ceramide synthase 4
signal peptide, CUB domain, EGF-like 1
carboxypeptidase E
parathyroid hormone-like peptide
arachidonate lipoxygenase, epidermal
patched homolog 2
stearoyl-Coenzyme A desaturase 1
dachsous 1 (Drosophila)
cytoplasmic FMR1 interacting protein 2
rhophilin, Rho GTPase binding protein 2
prion protein dublet
chemokine (C-X-C motif) receptor 4
chemokine (C-X-C motif) ligand 9
SET binding protein 1
leucine-rich repeat LGI family, member 2
NM_013599
NM_001081037
NM_010217
NM_144552
NM_026058
NM_022723
NM_013494
NM_008970
NM_145684
NM_008958
NM_009127
NM_001162943
NM_133769
NM_027897
NM_023043
NM_009911
NM_008599
NM_053099
NM_144945
2.53534
2.53366
2.50581
2.50082
2.47589
2.46246
2.4328
2.42713
2.42105
2.39458
2.37643
2.33643
2.32122
2.31369
2.3072
2.30564
2.28395
2.25846
2.2534
Development • Supplementary information
Development 143: doi:10.1242/dev.130898: Supplementary information
Sox9
Fgfr1
Runx1
Fndc1
Eif4e3
Heg1
Lhx2
Lrp4
Ccdc85a
Zdhhc2
Mill1
Micalcl
Pstpip2
Il2rg
Bnc2
Mybpc1
Cabp1
Kcnh3
Syt5
Fam13a
Grik4
1110012J17Rik
Plk3
Cxcl10
Ptch1
Alcam
Tgfb1
Vldlr
Mpa2l
Wnt10b
Trib1
Arhgef3
H2-Ab1
C130021I20Rik
Mtmr10
Dab1
Wnt2b
Stx11
Sv2b
SRY-box containing gene 9
fibroblast growth factor receptor 1
runt related transcription factor 1
fibronectin type III domain containing 1
eukaryotic translation initiation factor 4E
member 3
HEG homolog 1 (zebrafish)
LIM homeobox protein 2
low density lipoprotein receptor-related protein
4
coiled-coil domain containing 85A
zinc finger, DHHC domain containing 2
MHC I like leukocyte 1
MICAL C-terminal like
proline-serine-threonine phosphataseinteracting protein 2
interleukin 2 receptor, gamma chain
basonuclin 2
myosin binding protein C, slow-type
calcium binding protein 1
potassium voltage-gated channel, subfamily H
(eag-related) member 3
synaptotagmin V
family with sequence similarity 13, member A
glutamate receptor, ionotropic, kainate 4
RIKEN cDNA 1110012J17 gene
polo-like kinase 3 (Drosophila)
chemokine (C-X-C motif) ligand 10
patched homolog 1
activated leukocyte cell adhesion molecule
transforming growth factor, beta 1
very low density lipoprotein receptor
macrophage activation 2 like
wingless related MMTV integration site 10b
tribbles homolog 1 (Drosophila)
Rho guanine nucleotide exchange factor (GEF) 3
histocompatibility 2, class II antigen A, beta 1
Riken cDNA C130021I20 gene
myotubularin related protein 10
disabled homolog 1 (Drosophila)
wingless related MMTV integration site 2b
syntaxin 11
synaptic vesicle glycoprotein 2 b
NM_011448
NM_010206
NM_001111023
NM_001081416
NM_025829
2.24712
2.2423
2.22868
2.21535
2.20993
NM_175256
NM_010710
NM_172668
2.1946
2.19298
2.18112
NM_181577
NM_178395
NM_153749
AB359922
NM_013831
2.1585
2.15626
2.14469
2.14146
2.08008
NM_013563
NM_172870
NM_175418
NM_013879
NM_010601
2.06742
2.05488
2.04995
2.0347
2.03291
NM_016908
NM_153574
NM_175481
NM_001114098
NM_013807
NM_021274
NM_008957
NM_009655
NM_011577
NM_013703
NM_194336
NM_011718
NM_144549
NM_027871
NM_207105
AK147796
NM_172742
NM_177259
NM_009520
NM_029075
NM_001109753
2.02779
1.99645
1.98605
1.98034
1.97215
1.96566
1.96207
1.93344
1.92935
1.92326
1.92065
1.91905
1.91708
1.91348
1.91304
1.90649
1.90315
1.89918
1.89907
1.89836
1.89017
Development • Supplementary information
Development 143: doi:10.1242/dev.130898: Supplementary information
Nfkbia
nuclear factor of kappa light polypeptide gene
enhancer in B-cells inhibitor alpha
NM_010907
1.88282
Rnf152
Fads2
Gli1
Pdzd2
6330403K07Rik
Nr3c2
Krt18
Etv5
Kcnh2
ring finger protein 152
fatty acid desaturase 2
GLI-Kruppel family member GLI1
PDZ domain containing 2
RIKEN cDNA 6330403K07 gene
nuclear receptor subfamily 3, groupC, member2
keratin 18
ets variant gene 5
potassium voltage-gated channel, subfamily H
(eag-related) member 2
prostaglandin I receptor (IP)
SH3 domain containing ring finger 3
PTK2 protein tyrosine kinase 2 beta
microtubule-associated protein 2
myotubularin related protein 7
roundabout homolog 2 (Drosophila)
kalirin, RhoGEF kinase
B-cell leukemia/lymphoma 3
T cell-interacting, activating receptor on
myeloid cells 1
RAS-like, estrogen-regulated, growth-inhibitor
placental growth factor
signal transducing adaptor family member 1
a disintegrin-like and metallopeptidase with
thrombospondin motifs 15
neuronatin
RIKEN cDNA 3110082D06 gene
pellino 2
unc-5 homolog B (C. elegans)
tetraspanin 5
UDP-N-acetyl-alpha-D-galactosamine: polypeptide N-acetylgalactosaminyltransferase 6
NM_178779
NM_019699
NM_010296
NM_001081064
NM_134022
NM_001083906
NM_010664
NM_023794
NM_013569
1.87965
1.87774
1.87315
1.86608
1.85268
1.83938
1.83723
1.8353
1.83401
NM_008967
NM_172788
NM_001162365
NM_001039934
NM_001040699
NM_175549
NM_177357
NM_033601
NM_177363
1.83208
1.8301
1.82897
1.82823
1.82822
1.82721
1.8251
1.82083
1.80831
NM_181988
NM_008827
NM_019992
NM_001024139
1.80721
1.80406
1.80181
1.78899
NM_010923
NM_028474
NM_033602
NM_029770
NM_019571
NM_001161767
1.78484
1.77842
1.77669
1.77391
1.77279
1.7722
pigeon homolog (Drosophila)
Kv channel-interacting protein 1
dystrophin related protein 2
neuropilin (NRP) and tolloid (TLL)-like 1
serine incorporator 2
BTB and CNC homology 2
prostaglandin E synthase
TAP binding protein
phospholipase C, beta 2
NM_175437
NM_027398
NM_010078
NM_144946
NM_172702
NM_001109661
NM_022415
NM_001025313
NM_177568
1.76624
1.76196
1.76107
1.75975
1.75794
1.75674
1.75584
1.75121
1.74533
Ptgir
Sh3rf3
Ptk2b
Mtap2
Mtmr7
Robo2
Kalrn
Bcl3
Tarm1
Rerg
Pgf
Stap1
Adamts15
Nnat
3110082D06Rik
Peli2
Unc5b
Tspan5
Galnt6
Pion
Kcnip1
Drp2
Neto1
Serinc2
Bach2
Ptges
Tapbp
Plcb2
Development • Supplementary information
Development 143: doi:10.1242/dev.130898: Supplementary information
Meis1
Ajap1
Sh3gl3
Sema3d
Meis homeobox 1
adherens junction associated protein 1
SH3-domain GRB2-like 3
sema domain, immunoglobulin domain (Ig),
short basic domain secreted (semaphorin) 3D
NM_010789
NM_001099299
NM_017400
NM_028882
1.73948
1.73929
1.73684
1.73535
Sox2
Hhip
Hoxc6
Tsku
Rtn1
Smox
Pxdn
AY512949
Rcn3
SRY-box containing gene 2
Hedgehog-interacting protein
homeobox C6
tsukushin
reticulon 1
spermine oxidase
peroxidasin homolog (Drosophila)
cDNA sequence AY512949
reticulocalbin 3, EF-hand calcium binding
domain
ring finger protein 32
interleukin 23, alpha subunit p19
copine V
slit homolog 3 (Drosophila)
sushi domain containing 4
ATPase, Na+/K+ transporting, beta 1
polypeptide
SRY-box containing gene 21
bone morphogenetic protein 2
RIKEN cDNA 2010300C02 gene
sema domain, immunoglobulin domain (Ig),
transmembrane domain (TM) and short
cytoplasmic domain, (Semaphorin) 4C
calcium channel, voltage-dependent, T type,
alpha 1H subunit
RIKEN cDNA 1110028C15 gene
DNA segment, Chr 19, ERATO Doi 652,
expressed
insulin-like growth factor binding protein 4
solute carrier organic anion transporter family,
member 3A1
contactin 2
predicted gene 5077
runt related transcription factor 2
C-type lectin domain family 2, member d
prostaglandin-endoperoxide synthase 2
ets homologous factor
hairless
ADP-ribosylation factor-like 6
NM_011443
NM_020259
NM_010465
NM_001168541
NM_153457
NM_001177833
NM_181395
AY512949
NM_026555
1.7348
1.73156
1.72724
1.72657
1.72548
1.72453
1.71855
1.71621
1.71433
NM_021470
NM_031252
NM_153166
NM_011412
NM_144796
NM_009721
1.711
1.70695
1.70401
1.70263
1.70162
1.69741
NM_177753
NM_007553
NM_028096
NM_001126047
1.69563
1.69554
1.68928
1.68679
NM_021415
1.68588
NM_001122738
BC107403
1.68216
1.68043
NM_010517
NM_023908
1.68001
1.67316
NM_177129
NM_173864
NM_001146038
NM_053109
NM_011198
NM_007914
NM_021877
NM_019665
1.66761
1.66026
1.65805
1.65631
1.65597
1.65559
1.65486
1.6485
Rnf32
Il23a
Cpne5
Slit3
Susd4
Atp1b1
Sox21
Bmp2
2010300C02Rik
Sema4c
Cacna1h
1110028C15Rik
D19Ertd652e
Igfbp4
Slco3a1
Cntn2
Gm5077
Runx2
Clec2d
Ptgs2
Ehf
Hr
Arl6
Development • Supplementary information
Development 143: doi:10.1242/dev.130898: Supplementary information
Nup210
Rnf122
Galnt14
nucleoporin 210
ring finger protein 122
UDP-N-acetyl-alpha-D-galactosamine: polypeptide N-acetylgalactosaminyltransferase 14
NM_018815
NM_175136
NM_027864
1.6388
1.63805
1.63479
Bcar3
Doc2b
Gpc2
Mfap2
Parp8
Csf1
Hpca
Robo1
Gata6
Slc2a4
breast cancer anti-estrogen resistance 3
double C2, beta
glypican 2 (cerebroglycan)
microfibrillar-associated protein 2
poly (ADP-ribose) polymerase family, member 8
colony stimulating factor 1 (macrophage)
hippocalcin
roundabout homolog 1 (Drosophila)
GATA binding protein 6
solute carrier family 2 (facilitated glucose
transporter) member 4
TNFAIP3 interacting protein 1
snail homolog 3 (Drosophila)
a disintegrin-like and metallopeptidase with
thrombospondin motifs 17
solute carrier family 39 (zinc transporter),
member 2
neurotensin receptor 1
stonin 2
carbohydrate (keratan sulfate Gal-6)
sulfotransferase 1
insulin-like growth factor binding protein 7
PDZ and LIM domain 4
fibronectin leucine rich transmembrane protein
1
ankyrin repeat domain 45
sodium channel, type IV, beta
interferon induced transmembrane protein 3
von Willebrand factor A domain containing 2
zinc finger protein 703
amyloid beta (A4) precursor-like protein 1
protocadherin 20
EF-hand domain family, member A2
cortexin 1
protocadherin beta 17
SRY-box containing gene 4
baculoviral IAP repeat-containing 3
protocadherin beta 16
glutamate receptor, ionotropic, AMPA3
(alpha 3)
NM_013867
NM_007873
NM_172412
NM_008546
NM_001081009
NM_007778
NM_010471
NM_019413
NM_010258
NM_009204
1.63365
1.63109
1.63104
1.6301
1.62741
1.62535
1.62412
1.62296
1.62065
1.61892
NM_021327
NM_013914
NM_001033877
1.61539
1.61109
1.61011
NM_001039676
1.60699
NM_018766
NM_175367
NM_023850
1.60654
1.60549
1.60363
NM_001159518
NM_019417
NM_201411
1.60225
1.6007
1.6
NM_028664
NM_001013390
NM_025378
NM_172840
NM_001101502
NM_007467
NM_178685
NM_030110
NM_183315
NM_053142
NM_009238
NM_007464
NM_053141
NM_016886
1.59378
1.59078
1.5882
1.58769
1.58643
1.58109
1.5777
1.57743
1.57693
1.5748
1.57435
1.56615
1.566
1.56142
Tnip1
Snai3
Adamts17
Slc39a2
Ntsr1
Ston2
Chst1
Igfbp7
Pdlim4
Flrt1
Ankrd45
Scn4b
Ifitm3
Vwa2
Zfp703
Aplp1
Pcdh20
Efha2
Ctxn1
Pcdhb17
Sox4
Birc3
Pcdhb16
Gria3
Development • Supplementary information
Development 143: doi:10.1242/dev.130898: Supplementary information
Itga8
Cobll1
Mpped1
Tnc
Fam134b
Bdnf
Pfn2
Ednra
Ltbp1
Orai2
Prkar1b
Oasl2
Pck2
Kcnj13
Lzts1
Grasp
Abhd12b
Olfr332
Olfr354
Slc8a2
H2-M2
Gpc4
Sema6a
Sfrp1
Tcerg1l
Prdm1
Pak1
1190007F08Rik
Soat1
Tgfb3
Rnf180
Capsl
Ppp1r3c
Arhgef4
Spo11
integrin alpha 8
Cobl-like 1
metallophosphoesterase domain containing 1
tenascin C
family with sequence similarity 134, member B
brain derived neurotrophic factor
profilin 2
endothelin receptor type A
latent transforming growth factor beta binding
protein 1
ORAI calcium release-activated calcium
modulator 2
protein kinase, cAMP dependent regulatory,
type I beta
2'-5' oligoadenylate synthetase-like 2
phosphoenolpyruvate carboxykinase 2
(mitochondrial)
potassium inwardly-rectifying channel,
subfamily J, member 13
leucine zipper, putative tumor suppressor 1
GRP1 (general receptor for phosphoinositides
1)-associated scaffold protein
NM_001001309
NM_177025
NM_172610
NM_011607
NM_001034851
NM_001048139
NM_019410
NM_010332
NM_019919
1.55968
1.55902
1.55823
1.55711
1.5547
1.55203
1.55202
1.55142
1.54781
NM_178751
1.54545
NM_008923
1.54434
NM_011854
NM_028994
1.5437
1.543
NM_001110227
1.54167
NM_199364
NM_019518
1.54108
1.54028
abhydrolase domain containing 12B
olfactory receptor 332
olfactory receptor 354
solute carrier family 8 (sodium/calcium
exchanger), member 2
histocompatibility 2, M region locus 2
glypican 4
sema domain, transmembrane domain (TM),
and cytoplasmic domian (semaphorin) 6A
ENSMUST00000095662
NM_001011770
NM_146939
NM_148946
1.53875
1.53477
1.53475
1.53388
NM_008204
NM_008150
NM_018744
1.53362
1.52993
1.52824
secreted frizzled-related protein 1
transcription elongation regulator 1-like
PR domain containing 1, with ZNF domain
p21 protein (Cdc42/Rac)-activated kinase 1
RIKEN cDNA 1190007F08 gene
sterol O-acyltransferase 1
transforming growth factor, beta 3
ring finger protein 180
calcyphosine-like
protein phosphatase 1, regulatory (inhibitor)
subunit 3C
Rho guanine nucleotide exchange factor (GEF) 4
sporulation protein, meiosis-specific, SPO11
NM_013834
NM_183289
NM_007548
NM_011035
NM_001163721
NM_009230
NM_009368
NM_027934
NM_029341
NM_016854
1.52721
1.52632
1.52515
1.52389
1.5194
1.51793
1.51763
1.51676
1.51458
1.5111
NM_183019
NM_012046
1.51105
1.51063
Development • Supplementary information
Development 143: doi:10.1242/dev.130898: Supplementary information
Development 143: doi:10.1242/dev.130898: Supplementary information
Chst11
Mylip
Lrrc56
Serpinb6b
Myo1e
Cav2
4831426I19Rik
Naaladl2
homolog
carbohydrate sulfotransferase 11
myosin regulatory light chain interacting protein
leucine rich repeat containing 56
serine (or cysteine) peptidase inhibitor, clade B,
member 6
myosin IE
caveolin 2
RIKEN cDNA 4831426I19 gene
N-acetylated alpha-linked acidic dipeptidase-like
2
NM_021439
NM_153789
NM_001172064
NM_011454
1.51022
1.50443
1.50368
1.5019
NM_181072
NM_016900
NM_001042699
XM_910834
1.50175
1.50146
1.50112
1.50034
Genes symbol
Dct
Fabp7
Kit
Ednrb
Mcoln3
Hba-a1
Hba-a2
Tyr
Si
Slc45a2
Mitf
Hbb-b1
Slc24a5
Gpnmb
Itga4
Slc7a8
Gjc3
Gabrb2
Cubn
Bace2
Pax3
Zeb2
Description
dopachrome tautomerase
fatty acid binding protein 7, brain
kit oncogene
endothelin receptor type B
mucolipin 3
hemoglobin alpha, adult chain 1
hemoglobin alpha, adult chain 2
tyrosinase
silver
solute carrier family 45, member 2
microphthalmia-associated transcription factor
hemoglobin, beta adult major chain
solute carrier family 24, member 5
glycoprotein (transmembrane) nmb
integrin alpha 4
solute carrier family 7 (cationic amino acid
transporter, light chain, L system) member 8
gap junction protein, gamma 3
gamma-aminobutyric acid (GABA) A receptor,
subunit beta 2
cubilin (intrinsic factor-cobalamin receptor)
beta-site APP-cleaving enzyme 2
paired box gene 3
zinc finger E-box binding homeobox 2
Ref_Seq
NM_010024
NM_021272
NM_001122733
NM_007904
NM_134160
NM_008218
NM_001083955
NM_011661
NM_021882
NM_053077
NM_001113198
NM_008220
NM_175034
NM_053110
NM_010576
NM_016972
Fold
change
-13.3986
-11.1386
-8.89564
-8.03849
-7.67076
-7.59276
-7.07394
-7.05902
-6.53347
-6.52809
-6.29898
-6.28766
-6.27844
-6.06478
-6.03604
-5.91936
NM_080450
NM_008070
-5.91203
-5.76314
NM_001081084
NM_019517
NM_008781
NM_015753
-5.7264
-5.30143
-5.15059
-5.10228
Development • Supplementary information
Genes enriched in the interfollicular epidermis (IFE) at E14.5:
Slc7a11
Gucy1b3
Shc4
Dsc1
Cd97
Pde8a
Cpa3
Ptprj
Eya1
Them5
Tm4sf1
Serpinb12
Abca12
1700086L19Rik
Ttyh2
Sox10
Bhlhe41
Pmp22
Cdh19
Aadacl2
Megf10
4833423E24Rik
Ddah1
Serpinb3a
Elovl4
Iqgap2
Krt77
Ace2
Serpinb3c
Mlana
Npy
Aff3
Dbpht2
Casp14
Plp1
Rdh12
solute carrier family 7 (cationic amino acid
transporter, light chain, L system) member 11
guanylate cyclase 1, soluble, beta 3
SHC (Src homology 2 domain containing) family,
member 4
desmocollin 1
CD97 antigen
phosphodiesterase 8A
carboxypeptidase A3, mast cell
protein tyrosine phosphatase, receptor type, J
eyes absent 1 homolog (Drosophila)
thioesterase superfamily member 5
transmembrane 4 superfamily member 1
serine (or cysteine) peptidase inhibitor, clade B
(ovalbumin) member 12
ATP-binding cassette, sub-family A (ABC1),
member 12
RIKEN cDNA 1700086L19 gene
tweety homolog 2 (Drosophila)
SRY-box containing gene 10
basic helix-loop-helix family, member e41
peripheral myelin protein 22
cadherin 19, type 2
arylacetamide deacetylase-like 2
multiple EGF-like-domains 10
RIKEN cDNA 4833423E24 gene
dimethylarginine dimethylaminohydrolase 1
serine (or cysteine) peptidase inhibitor, clade B
(ovalbumin) member 3
elongation of very long chain fatty acids
(FEN1/Elo2, SUR4/Elo3, Yeast)-Like 4
IQ motif containing GTPase activating protein 2
keratin 77
angiotensin I converting enzyme (peptidyldipeptidase A) 2
serine (or cysteine) peptidase inhibitor, clade B,
member 3
melan-A
neuropeptide Y
AF4/FMR2 family, member 3
DNA binding protein with his-thr domain
caspase 14
Nproteolipid protein (myelin) 1
retinol dehydrogenase 12
NM_011990
-5.00851
NM_017469
NM_199022
-4.68383
-4.51824
NM_013504
NM_011925
NM_008803
NM_007753
NM_008982
NM_010164
NM_025416
NM_008536
NM_027971
-4.29284
-4.08062
-4.01469
-3.96657
-3.86641
-3.82696
-3.79337
-3.7218
-3.55006
NM_175210
-3.54327
NR_030733
NM_053273
NM_011437
NM_024469
NM_008885
NM_001081386
NM_001128091
NM_001001979
NM_001081664
NM_026993
NM_009126
-3.53514
-3.48151
-3.40337
-3.36134
-3.35803
-3.33919
-3.31869
-3.285
-3.28403
-3.27234
-3.19283
NM_148941
-3.17368
NM_027711
NM_001003667
NM_027286
-3.1546
-3.07428
-3.06103
NM_201363
-2.99416
NM_029993
NM_023456
NM_010678
NM_198866
NM_009809
NM_011123
NM_030017
-2.96325
-2.94426
-2.91408
-2.88289
-2.86772
-2.85823
-2.85649
Development • Supplementary information
Development 143: doi:10.1242/dev.130898: Supplementary information
Cdh2
Foxd3
Ptgds
Fap
Krtdap
Sdr16c6
Car8
Cttnbp2
Bpil2
Dmkn
Gabrb3
Muc15
Glcci1
Dock5
Tgm3
Vim
Ets1
Lix1l
Smpdl3a
Glrb
Pnpla1
Rhoj
Lmo2
Gpr124
Eng
Cyp4f39
Hspb1
Dsg1a
Gabra1
Rassf2
Fndc3c1
Mef2c
Pla2g2f
Krt1
Cyp2j6
Gpm6a
cadherin 2
forkhead box D3
prostaglandin D2 synthase (brain)
fibroblast activation protein
keratinocyte differentiation associated protein
short chain dehydrogenase/reductase family
16C, member 6
carbonic anhydrase 8
cortactin binding protein 2
bactericidal/permeability-increasing proteinlike 2
dermokine
gamma-aminobutyric acid (GABA) A receptor,
subunit beta 3
mucin 15
glucocorticoid induced transcript 1
dedicator of cytokinesis 5
transglutaminase 3, E polypeptide
vimentin
E26 avian leukemia oncogene 1, 5' domain
Lix1-like
sphingomyelin phosphodiesterase, acid-like 3A
glycine receptor, beta subunit
patatin-like phospholipase domain
containing 1
ras homolog gene family, member J
LIM domain only 2
G protein-coupled receptor 124
endoglin
cytochrome P450, family 4, subfamily f,
polypeptide 39
heat shock protein 1
desmoglein 1 alpha
gamma-aminobutyric acid (GABA) A receptor,
subunit alpha 1
Ras association (RalGDS/AF-6) domain family
member 2
fibronectin type III domain containing 3C1
myocyte enhancer factor 2C
phospholipase A2, group IIF
keratin 1
cytochrome P450, family 2, subfamily j,
polypeptide 6
glycoprotein m6a
NM_007664
NM_010425
NM_008963
NM_007986
NM_001033131
NM_001080710
-2.84678
-2.80057
-2.7837
-2.78074
-2.73273
-2.693
NM_007592
NM_080285
NM_177772
-2.68262
-2.6631
-2.65552
NM_001166173
NM_008071
-2.65336
-2.62234
NM_172979
NM_133236
NM_177780
NM_009374
NM_011701
NM_011808
NM_001163170
NM_020561
NM_010298
NM_001034885
-2.61603
-2.59503
-2.56376
-2.56111
-2.55643
-2.54204
-2.53879
-2.53731
-2.53534
-2.52928
NM_023275
NM_008505
NM_054044
NM_001146350
NM_177307
-2.52197
-2.51665
-2.51493
-2.51234
-2.47551
NM_013560
NM_010079
NM_010250
-2.46524
-2.4552
-2.44598
NM_175445
-2.40868
NM_001007580
NM_001170537
NM_012045
NM_008473
NM_010008
-2.39585
-2.39039
-2.37833
-2.37567
-2.36934
NM_153581
-2.36615
Development • Supplementary information
Development 143: doi:10.1242/dev.130898: Supplementary information
Cd44
2610528A11Rik
Serpinb3b
Ly6g6c
Syt4
Aox4
Dusp4
Cyp2w1
Tspan10
Gpr111
Lgals9
Krt10
Acsl1
C130079G13Rik
Sdr16c5
Dgat2
Tspan7
Ceacam1
Plxna4
Mgst1
Tmem45a
Ephx3
Igf1
Nkd2
Gpr155
Mgll
Loxl3
Lgals3
Dhrs7
Defb1
Igsf11
Apod
Ano7
Msn
Gsta1
Alx1
Qpct
CD44 antigen
RIKEN cDNA 2610528A11 gene
serine (or cysteine) peptidase inhibitor, clade B
(ovalbumin) member 3
lymphocyte antigen 6 complex, locus G6C
synaptotagmin IV
aldehyde oxidase 4
dual specificity phosphatase 4
cytochrome P450, family 2, subfamily w,
polypeptide 1
tetraspanin 10
G protein-coupled receptor 111
lectin, galactose binding, soluble 9
keratin 10
acyl-CoA synthetase long-chain family member
1
RIKEN cDNA C130079G13 gene
short chain dehydrogenase/reductase family
16C, member 5
diacylglycerol O-acyltransferase 2
tetraspanin 7
carcinoembryonic antigen-related cell adhesion
molecule 1
plexin A4
microsomal glutathione S-transferase 1
transmembrane protein 45a
epoxide hydrolase 3
insulin-like growth factor 1
naked cuticle 2 homolog (Drosophila)
G protein-coupled receptor 155
monoglyceride lipase
lysyl oxidase-like 3
lectin, galactose binding, soluble 3
dehydrogenase/reductase (SDR family)
member 7
defensin beta 1
immunoglobulin superfamily, member 11
apolipoprotein D
anoctamin 7
moesin
glutathione S-transferase, alpha 1 (Ya)
ALX homeobox 1
glutaminyl-peptide cyclotransferase (glutaminyl
cyclase)
NM_009851
BC049685
NM_198680
-2.36345
-2.35047
-2.34213
NM_023463
NM_009308
NM_023631
NM_176933
NM_001160265
-2.33239
-2.32023
-2.29538
-2.28567
-2.28215
NM_145363
NM_001033493
NM_010708
NM_010660
NM_007981
-2.2754
-2.24943
-2.24754
-2.24585
-2.24443
NM_177661
NM_181989
-2.2349
-2.23471
NM_026384
NM_019634
NM_001039185
-2.22619
-2.22509
-2.21668
NM_175750
NM_019946
NM_019631
NM_001033163
NM_010512
NM_028186
NM_001080707
NM_001166251
NM_013586
NM_001145953
NM_025522
-2.21437
-2.21317
-2.21307
-2.20599
-2.19222
-2.18762
-2.17668
-2.1652
-2.16268
-2.15513
-2.14505
NM_007843
NM_170599
NM_007470
NM_207031
NM_010833
NM_008181
NM_172553
NM_027455
-2.13563
-2.13439
-2.12285
-2.11815
-2.11068
-2.10006
-2.07513
-2.05609
Development • Supplementary information
Development 143: doi:10.1242/dev.130898: Supplementary information
Pcsk2
Lox
Tgm1
Rxrg
Itga9
Fam174b
Trf
St8sia6
Tmem26
Dpysl3
Myo7a
Chsy3
Dsg1b
Hsd17b11
Npbwr1
Clvs1
Gca
Mocos
Gm10639
Mme
Fmn1
Gsta2
Nipal1
Rab25
Gldc
F3
Pde3a
Slc6a15
Scel
Atg4a
Nipal4
St3gal5
Tprg
Plxnc1
Pcsk6
Vat1l
Phyhipl
Hexa
Fam13c
proprotein convertase subtilisin/kexin type 2
lysyl oxidase
transglutaminase 1, K polypeptide
retinoid X receptor gamma
integrin alpha 9
family with sequence similarity 174, member B
transferrin
ST8 alpha-N-acetyl-neuraminide alpha-2,8sialyltransferase 6
transmembrane protein 26
dihydropyrimidinase-like 3
myosin VIIA
chondroitin sulfate synthase 3
desmoglein 1 beta
hydroxysteroid (17-beta) dehydrogenase 11
neuropeptides B/W receptor 1
clavesin 1
grancalcin
molybdenum cofactor sulfurase
predicted gene 10639
membrane metallo endopeptidase
formin 1
glutathione S-transferase, alpha 2 (Yc2)
NIPA-like domain containing 1
RAB25, member RAS oncogene family
glycine decarboxylase
coagulation factor III
phosphodiesterase 3A, cGMP inhibited
solute carrier family 6 (neurotransmitter
transporter), member 15
sciellin
autophagy-related 4A (yeast)
NIPA-like domain containing 4
ST3 beta-galactoside alpha-2,3-sialyltransferase
5
transformation related protein 63 regulated
plexin C1
proprotein convertase subtilisin/kexin type 6
vesicle amine transport protein 1 homolog-like
phytanoyl-CoA hydroxylase interacting proteinlike
hexosaminidase A
family with sequence similarity 13, member C
NM_008792
NM_010728
NM_001161715
NM_009107
NM_133721
NM_001162532
NM_133977
NM_145838
-2.04744
-2.04368
-2.01038
-2.00772
-2.00334
-1.99666
-1.99192
-1.99135
NM_177794
NM_009468
NM_008663
NM_001081328
NM_181682
NM_053262
NM_010342
NM_028940
NM_145523
NM_026779
NM_001122660
NM_008604
NM_010230
NM_008182
NM_001081205
NM_016899
NM_138595
NM_010171
NM_018779
NM_175328
-1.99127
-1.98497
-1.98315
-1.98098
-1.97908
-1.97763
-1.9776
-1.97621
-1.97335
-1.9684
-1.96733
-1.95696
-1.95256
-1.93678
-1.93147
-1.93048
-1.92331
-1.92279
-1.92154
-1.92055
NM_022886
NM_174875
NM_172524
NM_011375
-1.91843
-1.91751
-1.89996
-1.89425
NM_175165
NM_018797
NM_011048
NM_173016
NM_178621
-1.89031
-1.88757
-1.88695
-1.88139
-1.88025
NM_010421
NM_024244
-1.87951
-1.87934
Development • Supplementary information
Development 143: doi:10.1242/dev.130898: Supplementary information
Acadl
Parvb
Gabrp
Smtnl2
Cpa6
Lipm
Dpp4
Anxa1
Afap1l2
Heyl
Zfp185
Atg4a
Ch25h
4931406C07Rik
Slc2a3
Col12a1
Sgip1
Adam12
Gulp1
Fam57a
Ccr4
Plagl1
Tmem154
St3gal1
Crmp1
Il22ra1
Cftr
Ctsc
Tnik
Sbsn
Chl1
Uap1l1
Pcbd1
acyl-Coenzyme A dehydrogenase, long-chain
parvin, beta
gamma-aminobutyric acid (GABA) A receptor,
pi
smoothelin-like 2
carboxypeptidase A6
lipase, family member M
dipeptidylpeptidase 4
annexin A1
actin filament associated protein 1-like 2
hairy/enhancer-of-split related with YRPW
motif-like
zinc finger protein 185
autophagy-related 4A (yeast)
cholesterol 25-hydroxylase
RIKEN cDNA 4931406C07 gene
solute carrier family 2 (facilitated glucose
transporter) member 3
collagen, type XII, alpha 1
SH3-domain GRB2-like (endophilin) interacting
protein 1
a disintegrin and metallopeptidase domain 12
(meltrin alpha)
GULP, engulfment adaptor PTB domain
containing 1
family with sequence similarity 57, member A
chemokine (C-C motif) receptor 4
pleiomorphic adenoma gene-like 1
transmembrane protein 154
ST3 beta-galactoside alpha-2,3-sialyltransferase
1
collapsin response mediator protein 1
interleukin 22 receptor, alpha 1
cystic fibrosis transmembrane conductance
regulator homolog
cathepsin C
TRAF2 and NCK interacting kinase
suprabasin
cell adhesion molecule with homology to
L1CAM
UDP-N-acteylglucosamine pyrophosphorylase
1-like 1
pterin 4 alpha carbinolamine
dehydratase/dimerization cofactor of
Hepatocyte Nuclear Factor 1 Alpha
NM_007381
NM_133167
NM_146017
-1.87602
-1.86923
-1.86752
NM_177776
NM_177834
NM_023903
NM_010074
NM_010730
NM_146102
NM_013905
-1.86721
-1.8646
-1.86238
-1.86079
-1.86048
-1.85728
-1.85722
NM_009549
NM_174875
NM_009890
NM_133732
NM_011401
-1.85238
-1.85005
-1.85
-1.848
-1.84559
NM_007730
NM_144906
-1.8431
-1.84309
NM_007400
-1.84139
NM_028450
-1.84102
NM_027773
NM_009916
NM_009538
NM_177260
NM_009177
-1.8401
-1.83905
-1.83139
-1.83136
-1.82318
NM_007765
NM_178257
NM_021050
-1.81883
-1.81498
-1.81473
NM_009982
NM_026910
NM_172205
NM_007697
-1.81255
-1.8114
-1.81113
-1.80492
NM_001033293
-1.79965
NM_025273
-1.79887
Development • Supplementary information
Development 143: doi:10.1242/dev.130898: Supplementary information
Pde3b
Arhgap6
Ceacam19
Adamts1
Rab31
Nppb
Cdh9
Adssl1
Edn1
Lypd3
Capns2
2310007B03Rik
Anxa8
Ppp1r16b
Rin3
Aim1
Gm5226
Ogn
Manba
2210023G05Rik
Slc26a7
Cd200
Rab3d
Leprel1
AW551984
C2
Scnn1a
Il15
Sirpa
Dlx5
Hist1h2bc
Nkain4
Dlc1
Alox12
Syngr1
Ptprm
Cd109
Cpt1a
Igfbp3
Edil3
phosphodiesterase 3B, cGMP-inhibited
Rho GTPase activating protein 6
carcinoembryonic antigen-related cell adhesion
molecule 19
a disintegrin-like and metallopeptidase reprolysin type with Thrombospondin Type 1 Motif, 1
RAB31, member RAS oncogene family
natriuretic peptide precursor type B
cadherin 9
adenylosuccinate synthetase like 1
endothelin 1
Ly6/Plaur domain containing 3
calpain, small subunit 2
RIKEN cDNA 2310007B03 gene
annexin A8
protein phosphatase 1, regulatory (inhibitor)
subunit 16
Ras and Rab interactor 3
absent in melanoma 1
predicted pseudogene 5226
osteoglycin
mannosidase, beta A, lysosomal
RIKEN cDNA 2210023G05 gene
solute carrier family 26, member 7
CD200 antigen
RAB3D, member RAS oncogene family
leprecan-like 1
expressed sequence AW551984
complement component 2 (within H-2S)
sodium channel, nonvoltage-gated 1 alpha
interleukin 15
signal-regulatory protein alpha
distal-less homeobox 5
histone cluster 1, H2bc
Na+/K+ transporting ATPase interacting 4
deleted in liver cancer 1
arachidonate 12-lipoxygenase
synaptogyrin 1
protein tyrosine phosphatase, receptor type, M
CD109 antigen
carnitine palmitoyltransferase 1a, liver
insulin-like growth factor binding protein 3
EGF-like repeats and discoidin I-like domains 3
NM_011055
NM_009707
NM_177036
-1.79598
-1.79047
-1.78945
NM_009621
-1.78818
NM_133685
NM_008726
NM_009869
NM_007421
NM_010104
NM_133743
NM_027112
NM_172411
NM_013473
NM_153089
-1.78794
-1.78734
-1.78631
-1.78417
-1.78375
-1.78152
-1.78084
-1.77783
-1.77481
-1.76265
NM_177620
NM_172393
XM_914955
NM_008760
NM_027288
NM_197999
NM_145947
NM_010818
NM_031874
NM_173379
NM_178737
NM_013484
NM_011324
NM_008357
NM_007547
NM_010056
NM_023422
NM_021426
NM_015802
NM_007440
NM_207708
NM_008984
NM_153098
NM_013495
NM_008343
NM_001037987
-1.7594
-1.75903
-1.75671
-1.75611
-1.75238
-1.7485
-1.7447
-1.744
-1.7392
-1.73852
-1.7381
-1.73393
-1.73157
-1.73129
-1.72769
-1.727
-1.72637
-1.72516
-1.71766
-1.71714
-1.71617
-1.71509
-1.70606
-1.70545
-1.70523
-1.7045
Development • Supplementary information
Development 143: doi:10.1242/dev.130898: Supplementary information
Prex1
Aebp1
Foxo1
Syde1
Ica1
Faah
Gsta3
Renbp
Gpr143
Rab27b
Cotl1
Gpr115
Pla2g4f
Creg1
Atp6v0a1
Fbn2
Cdkn1a
Abtb2
Vat1
Agtr1a
Rarb
Tmbim1
Myo5b
Sdc3
Fam83a
Aldh1a7
Npl
Nkd1
Mall
Reln
Rhob
Gm2a
Plbd1
Gm6181
Prkg2
Fez1
Ppfibp2
phosphatidylinositol-3,4,5-trisphosphatedependent Rac exchange factor 1
AE binding protein 1
forkhead box O1
synapse defective 1, Rho GTPase, homolog 1 (C.
elegans)
islet cell autoantigen 1
fatty acid amide hydrolase
glutathione S-transferase, alpha 3
renin binding protein
G protein-coupled receptor 143
RAB27b, member RAS oncogene family
coactosin-like 1 (Dictyostelium)
G protein-coupled receptor 115
phospholipase A2, group IVF
cellular repressor of E1A-stimulated genes 1
ATPase, H+ transporting, lysosomal V0 subunit
A1
fibrillin 2
cyclin-dependent kinase inhibitor 1A (P21)
ankyrin repeat and BTB (POZ) domain
containing 2
vesicle amine transport protein 1 homolog (T
californica)
angiotensin II receptor, type 1a
retinoic acid receptor, beta
transmembrane BAX inhibitor motif containing
1
myosin VB
syndecan 3
family with sequence similarity 83, member A
aldehyde dehydrogenase family 1, subfamily A7
N-acetylneuraminate pyruvate lyase
naked cuticle 1 homolog (Drosophila)
mal, T-cell differentiation protein-like
reelin
ras homolog gene family, member B
GM2 ganglioside activator protein
phospholipase B domain containing 1
predicted pseudogene 6181
protein kinase, cGMP-dependent, type II
fasciculation and elongation protein zeta 1
(zygin I)
PTPRF interacting protein, binding protein 2
NM_177782
-1.70439
NM_009636
NM_019739
NM_027875
-1.70392
-1.70091
-1.69704
NM_010492
NM_010173
NM_001077353
NM_023132
NM_010951
NM_001082553
NM_028071
NM_030067
NM_001024145
NM_011804
NM_016920
-1.69649
-1.69601
-1.69572
-1.69342
-1.6893
-1.68653
-1.68495
-1.68479
-1.6837
-1.68105
-1.68015
NM_010181
NM_007669
NM_178890
-1.67988
-1.67904
-1.67736
NM_012037
-1.67695
NM_177322
NM_011243
NM_027154
-1.67621
-1.67254
-1.66823
NM_201600
NM_011520
NM_173862
NM_011921
NM_028749
NM_027280
NM_145532
NM_011261
NM_007483
NM_010299
NM_025806
XM_885168
NM_008926
NM_183171
-1.6682
-1.66804
-1.66613
-1.65783
-1.65692
-1.65403
-1.65312
-1.65289
-1.6515
-1.64723
-1.64712
-1.64469
-1.64465
-1.64201
NM_008905
-1.64072
Development • Supplementary information
Development 143: doi:10.1242/dev.130898: Supplementary information
Development 143: doi:10.1242/dev.130898: Supplementary information
Id2
Mxra7
Ap1s2
Slc27a6
Gfra1
Serpinb7
4930485B16Rik
Npr2
Fads3
Ankrd22
Bend6
Cpeb4
Nipal2
Cpne4
Serpina3b
1700055N04Rik
Gm10786
Ppl
Lta4h
Lpcat2
Tmem108
Ttc22
Fmod
Sat1
Lipk
Shc3
Ahr
Gucy1a3
Dsg3
Tdrkh
natriuretic peptide receptor 2
fatty acid desaturase 3
ankyrin repeat domain 22
BEN domain containing 6
cytoplasmic polyadenylation element binding
protein 4
NIPA-like domain containing 2
copine IV
serine (or cysteine) peptidase inhibitor, clade A,
member 3
RIKEN cDNA 1700055N04 gene
predicted gene 10786
periplakin
leukotriene A4 hydrolase
lysophosphatidylcholine acyltransferase 2
transmembrane protein 108
tetratricopeptide repeat domain 22
fibromodulin
spermidine/spermine N1-acetyl transferase 1
lipase, family member K
src homology 2 domain-containing
transforming protein C3
aryl-hydrocarbon receptor
guanylate cyclase 1, soluble, alpha 3
desmoglein 3
tudor and KH domain containing protein
NM_008555
NM_001081390
NM_001083894
NM_019835
-1.64019
-1.63705
-1.6357
-1.63195
NM_010496
NM_026280
NM_026887
-1.63144
-1.63076
-1.62928
NM_001081072
-1.62671
NM_010279
-1.62607
NM_027548
-1.62578
ENSMUST0000006770
5
NM_173788
NM_021890
NM_024204
NM_177235
NM_026252
-1.62514
NM_145469
NM_028719
NM_173024
-1.62162
-1.62158
-1.62112
AK081788
ENSMUST0000009955
0
NM_008909
NM_008517
NM_173014
NM_178638
NM_177667
NM_021355
NM_009121
NM_172837
NM_009167
-1.62076
-1.61909
NM_013464
NM_021896
NM_030596
NM_028307
-1.60638
-1.60579
-1.6046
-1.60207
-1.62372
-1.62337
-1.62334
-1.6224
-1.62213
-1.61745
-1.61696
-1.61627
-1.61446
-1.6136
-1.6126
-1.61253
-1.61147
-1.60699
Development • Supplementary information
Masp1
Palld
Liph
B4galt5
(liprin beta 2)
mannan-binding lectin serine peptidase 1
palladin, cytoskeletal associated protein
lipase, member H
UDP-Gal:betaGlcNAc beta 1,4galactosyltransferase, polypeptide 5
inhibitor of DNA binding 2
matrix-remodelling associated 7
adaptor-related protein complex 1, sigma 2
subunit
solute carrier family 27 (fatty acid transporter),
member 6
glial cell line derived neurotrophic factor family
receptor alpha 1
serine (or cysteine) peptidase inhibitor, clade B,
member 7
RIKEN cDNA 4930485B16 gene
Development 143: doi:10.1242/dev.130898: Supplementary information
Grhl1
Thrb
Ehd4
Klf3
Col8a1
Hoxc13
Aqp3
Irak4
Gm106
Cbs
Dock10
I730030J21Rik
Rnf128
Mlph
Tacc1
Sult2b1
Mrps21
Il1f5
Pip5k1b
Cd63
Egfl6
Dnase1l3
Itm2a
Susd2
D7Ertd443e
Maob
Cldn1
Nid1
5430435G22Rik
Nceh1
Eef2k
Ostf1
tumor-associated calcium signal transducer 2
tec protein tyrosine kinase
selenocysteine lyase
melanocortin 1 receptor
G protein-coupled receptor 87
kelch-like 30 (Drosophila)
dapper homolog 1, antagonist of beta-catenin
(xenopus)
grainyhead-like 1 (Drosophila)
thyroid hormone receptor beta
EH-domain containing 4
Kruppel-like factor 3 (basic)
collagen, type VIII, alpha 1
homeobox C13
aquaporin 3
interleukin-1 receptor-associated kinase 4
predicted gene 106
cystathionine beta-synthase
dedicator of cytokinesis 10
RIKEN cDNA I730030J21 gene
ring finger protein 128
melanophilin
transforming, acidic coiled-coil containing
protein 1
sulfotransferase family, cytosolic, 2B, member
1
mitochondrial ribosomal protein S21
interleukin 1 family, member 5 (delta)
phosphatidylinositol-4-phosphate 5-kinase,
type 1 beta
CD63 antigen
EGF-like-domain, multiple 6
deoxyribonuclease 1-like 3
integral membrane protein 2A
sushi domain containing 2
DNA segment, Chr 7, ERATO Doi 443, expressed
monoamine oxidase B
claudin 1
nidogen 1
RIKEN cDNA 5430435G22 gene
arylacetamide deacetylase-like 1
eukaryotic elongation factor-2 kinase
osteoclast stimulating factor 1
NM_020047
NM_001113460
NM_016717
NM_008559
NM_032399
NM_027551
NM_021532
-1.60099
-1.60042
-1.59996
-1.59962
-1.59921
-1.59911
-1.59768
NM_001161406
NM_009380
NM_133838
NM_008453
NM_007739
NM_010464
NM_016689
NM_029926
NM_001033288
NM_144855
NM_175291
ENSMUST0000008925
2
NM_023270
NM_053015
NM_177089
-1.59755
-1.59645
-1.5963
-1.5948
-1.5946
-1.59267
-1.59194
-1.59068
-1.58707
-1.58694
-1.58613
-1.58459
NM_017465
-1.57843
NM_078479
NM_001146087
NM_008846
-1.57721
-1.57106
-1.5667
NM_001042580
NM_019397
NM_007870
NM_008409
NM_027890
GQ499374
NM_172778
NM_016674
NM_010917
NM_145509
NM_178772
NM_007908
NM_017375
-1.56621
-1.56356
-1.56243
-1.56183
-1.55929
-1.55884
-1.5574
-1.55157
-1.5506
-1.55016
-1.5486
-1.54467
-1.54424
-1.58383
-1.58285
-1.58058
Development • Supplementary information
Tacstd2
Tec
Scly
Mc1r
Gpr87
Klhl30
Dact1
Serpinb3d
Trim71
Lgals12
D030046N08Ri
k
Cds1
Lactb2
Runx3
Abhd14b
Tinagl1
Aldh3b2
Sgpp1
Ndrg2
Fam178b
9530008L14Rik
Depdc6
Elavl4
Kcnk6
Trpc1
Pdzk1ip1
Tubb3
Paqr5
Vegfc
Myc
Trim2
Trpm1
Gstm6
Gsdmc
Rapgefl1
Tmem184a
Car6
Krt15
Dsc2
Tcn2
Gstp2
Lce6a
Vcan
serine (or cysteine) peptidase inhibitor, clade B
(ovalbumin) member 3
tripartite motif-containing 71
lectin, galactose binding, soluble 12
RIKEN cDNA D030046N08 gene
NM_201376
-1.54375
NM_001042503
NM_019516
AK141732
-1.54353
-1.5435
-1.54326
CDP-diacylglycerol synthase 1
lactamase, beta 2
runt related transcription factor 3
abhydrolase domain containing 14b
tubulointerstitial nephritis antigen-like 1
aldehyde dehydrogenase 3 family, member B2
sphingosine-1-phosphate phosphatase 1
N-myc downstream regulated gene 2
family with sequence similarity 178, member B
RIKEN cDNA 9530008L14 gene
DEP domain containing 6
ELAV (embryonic lethal, abnormal vision,
Drosophila)-like 4
potassium inwardly-rectifying channel,
subfamily K, member 6
transient receptor potential cation channel,
subfamily C, member 1
PDZK1 interacting protein 1
tubulin, beta 3
progestin and adipoQ receptor family member
V
vascular endothelial growth factor C
myelocytomatosis oncogene
tripartite motif-containing 2
transient receptor potential cation channel,
subfamily M, member 1
glutathione S-transferase, mu 6
gasdermin C
Rap guanine nucleotide exchange factor (GEF)like 1
transmembrane protein 184a
carbonic anhydrase 6
keratin 15
desmocollin 2
transcobalamin 2
glutathione S-transferase, pi 2
late cornified envelope 6A
versican
NM_173370
NM_145381
NM_019732
NM_029631
NM_023476
NM_001177438
NM_030750
NM_013864
NM_201365
NM_175417
NM_001037937
NM_010488
-1.54218
-1.5418
-1.54153
-1.54123
-1.53826
-1.53793
-1.53666
-1.5341
-1.53347
-1.53333
-1.53249
-1.53164
NM_001033525
-1.53139
NM_011643
-1.53134
NM_001164557
NM_023279
NM_028748
-1.52907
-1.5283
-1.52822
NM_009506
NM_010849
NM_030706
NM_001039104
-1.52594
-1.52588
-1.52511
-1.52394
NM_008184
NM_031378
NM_001080925
-1.52352
-1.52268
-1.52242
NM_001161548
NM_009802
NM_008469
NM_013505
NM_015749
NM_181796
NM_001166172
NM_001081249
-1.52236
-1.52167
-1.51893
-1.51662
-1.51643
-1.51642
-1.51564
-1.5153
Development • Supplementary information
Development 143: doi:10.1242/dev.130898: Supplementary information
Ahnak2
Retsat
Rapgef4
Gltp
Mcam
Sdr42e1
Mmp16
Sec11c
Ltbr
Sptlc3
Thbd
Il17rc
Prrg4
2210411K11Rik
Il1rap
Maoa
Notch3
Lmo4
AHNAK nucleoprotein 2
retinol saturase all trans retinol 13,14 reductase
Rap guanine nucleotide exchange factor (GEF) 4
glycolipid transfer protein
melanoma cell adhesion molecule
short chain dehydrogenase/reductase family
42E, member 1
matrix metallopeptidase 16
SEC11 homolog C (S. cerevisiae)
lymphotoxin B receptor
serine palmitoyltransferase, long chain base
subunit 3
thrombomodulin
interleukin 17 receptor C
proline rich Gla (G-carboxyglutamic acid) 4
(transmembrane)
RIKEN cDNA 2210411K11 gene
interleukin 1 receptor accessory protein
monoamine oxidase A
Notch gene homolog 3 (Drosophila)
LIM domain only 4
BC138468
NM_026159
NM_019688
NM_019821
NM_023061
NM_028725
-1.51427
-1.51347
-1.51327
-1.51324
-1.51124
-1.51123
NM_019724
NM_025468
NM_010736
NM_175467
-1.51108
-1.51074
-1.50968
-1.50781
NM_009378
NM_134159
NM_178695
-1.50665
-1.50461
-1.50406
NM_029384
NM_008364
NM_173740
NM_008716
NM_010723
-1.50405
-1.50257
-1.50129
-1.50126
-1.5007
Development • Supplementary information
Development 143: doi:10.1242/dev.130898: Supplementary information
Development 143: doi:10.1242/dev.130898: Supplementary information
Supplementary Table S2. Representative lists of differentially regulated genes in the epidermis of N
embryos when compared to controls at E14.5 (a, downregulated and b, upregulated in N embryos vs.
controls). Only mRNAs differentially up- or down-regulated ≥ 1.5x are listed.
Differentially expressed genes in ∆N embryos at E14.5
Downregulated in ∆N embryos:
Genes symbol
Description
Ref_Seq
Frem1
Fras1 related extracellular matrix protein 1
NM_177863
Fold
change
5.3297
Tnc
tenascin C
NM_011607
4.18183
Cd74
CD74 Antigen
NM_001042605
3.83445
Prnd
prion protein dublet
NM_023043
3.69287
Socs2
suppressor of cytokine signaling 2
NM_007706
3.64399
Dkk4
dickkopf homolog 4 (Xenopus laevis)
NM_145592
3.59292
Pla2g7
NM_013737
3.51707
Slc14a1
phospholipase A2, group VII (platelet-activating factor
acetylhydrolase, plasma)
solute carrier family 14 (urea transporter), member 1
NM_001171010
3.42343
Ly6g6c
lymphocyte antigen 6 complex, locus G6C
NM_023463
3.03654
Foxi3
forkhead box I3
NM_001101464
2.90417
Serpinb3a
NM_009126
2.85518
Susd2
serine (or cysteine) peptidase inhibitor, clade B
(ovalbumin) member 3
sushi domain containing 2
NM_027890
2.82966
Ptch1
patched homolog 1
NM_008957
2.82694
BC100530
cDNA sequence BC100530
NM_001082546
2.80312
Wif1
Wnt inhibitory factor 1
NM_011915
2.77261
Clca2
chloride channel calcium activated 2
NM_030601
2.69697
Nrp2
neuropilin 2
NM_001077403
2.64097
Necab1
N-terminal EF-hand calcium binding protein 1
NM_178617
2.63714
Lypd5
Ly6/Plaur domain containing 5
NM_029806
2.54125
Gli1
GLI-Kruppel family member GLI1
NM_010296
2.49257
Trps1
trichorhinophalangeal syndrome I (human)
NM_032000
2.47674
Dusp6
dual specificity phosphatase 6
NM_026268
2.46991
Il2rg
interleukin 2 receptor, gamma chain
NM_013563
2.4657
Tspan18
tetraspanin 18
NM_183180
2.4343
Serpinb2
NM_001174170
2.39753
Tnf
serine (or cysteine) peptidase inhibitor, clade B,
memebr 2
tumor necrosis factor
NM_013693
2.38059
Acer1
alkaline ceramidase 1
NM_175731
2.37223
Development • Supplementary information
a)
Adamts3
NM_177872
2.21406
C1s
a disintegrin-like and metallopeptidase with
thrombospondin motifs 3
complement component 1, s subcomponent
NM_144938
2.21217
Rragd
Ras-related GTP binding D
NM_027491
2.20995
Ltb
lymphotoxin B
NM_008518
2.20462
Tprg
transformation related protein 63 regulated
NM_175165
2.17802
Sprr1b
small proline-rich protein 1B
NM_009265
2.16581
Stfa1
stefin A1
NM_001082543
2.16379
2610528A11Ri
k
Sdr9c7
RIKEN cDNA 2610528A11 gene
BC049685
2.13002
NM_027301
2.12331
Ptch2
4short chain dehydrogenase/reductase family 9C,
member 7
patched homolog 2
NM_008958
2.11929
Ncam1
neural cell adhesion molecule 1
NM_001081445
2.11752
Sostdc1
sclerostin domain containing 1
NM_025312
2.10836
Krt77
keratin 77
NM_001003667
2.0926
Prss35
protease, serine, 35
NM_178738
2.05754
Srgap1
SLIT-ROBO Rho GTPase activating protein 1
NM_001081037
2.04739
Fndc1
fibronectin type III domain containing 1
NM_001081416
2.01216
D19Ertd652e
DNA segment, Chr 19, ERATO Doi 652, expressed
BC107403
1.98524
4833423E24Ri
k
Aox4
RIKEN cDNA 4833423E24 gene
NM_001081664
1.98148
aldehyde oxidase 4
NM_023631
1.97771
Tnfaip3
tumor necrosis factor, alpha-induced protein 3
NM_009397
1.94167
Galnt6
UDP-N-acetyl-alpha-D-galactosamine: polypeptide
N-acetylgalactosaminyltransferase 6
NM_001161767
1.91422
2210023G05Ri
k
Fgd5
RIKEN cDNA 2210023G05 gene
NM_197999
1.90753
FYVE, RhoGEF and PH domain containing 5
NM_172731
1.90493
Eif4e3
eukaryotic translation initiation factor 4E member 3
NM_025829
1.89894
Cyfip2
cytoplasmic FMR1 interacting protein 2
NM_133769
1.89842
Ifitm1
interferon induced transmembrane protein 1
NM_026820
1.89673
Cntnap1
contactin associated protein-like 1
NM_016782
1.89603
Egln3
EGL nine homolog 3 (C. elegans)
NM_028133
1.88526
Bcar3
breast cancer anti-estrogen resistance 3
NM_013867
1.86971
Shh
sonic hedgehog
NM_009170
1.86585
Madcam1
mucosal vascular addressin cell adhesion molecule 1
NM_013591
1.86208
Mical2
microtubule associated monoxygenase, calponin and
LIM domain containing 2
very low density lipoprotein receptor
NM_177282
1.84081
NM_013703
1.83891
Vldlr
Development • Supplementary information
Development 143: doi:10.1242/dev.130898: Supplementary information
Robo2
roundabout homolog 2 (Drosophila)
NM_175549
1.83432
Cyp17a1
NM_007809
1.83325
Lor
cytochrome P450, family 17, subfamily a, polypeptide
1
loricrin
NM_008508
1.83189
Stfa3
stefin A3
NM_025288
1.82883
Serpinb3b
NM_198680
1.82336
Clca1
serine (or cysteine) peptidase inhibitor, clade B
(ovalbumin) member 3
chloride channel calcium activated 1
NM_009899
1.82303
Cnfn
cornifelin
NM_028219
1.81784
Serpinb3c
NM_201363
1.80208
NM_181989
1.79991
NM_008815
1.79859
Chl1
serine (or cysteine) peptidase inhibitor, clade B
(ovalbumin) member 3
short chain dehydrogenase/reductase family 16C,
member 5
ets variant gene 4 (E1A enhancer binding protein,
E1AF)
cell adhesion molecule with homology to L1CAM
NM_007697
1.78983
Mmp9
matrix metallopeptidase 9
NM_013599
1.78771
Moxd1
monooxygenase, DBH-like 1
NM_021509
1.78575
Etv5
ets variant gene 5
NM_023794
1.77897
1600029D21Ri
k
Alox12b
RIKEN cDNA 1600029D21 gene
NM_029639
1.7675
arachidonate 12-lipoxygenase, 12R type
NM_009659
1.7653
Tmem45a
transmembrane protein 45a
NM_019631
1.76028
Bcl3
B-cell leukemia/lymphoma 3
NM_033601
1.75433
Rgs5
regulator of G-protein signaling 5
NM_009063
1.72895
Astl
astacin-like metalloendopeptidase (M12 family)
NM_172539
1.72024
Lgals3
lectin, galactose binding, soluble 3
NM_001145953
1.71812
Ndufa4l2
NM_001098789
1.71246
Prokr2
NADH dehydrogenase (ubiquinone) 1 alpha
subcomplex, 4-like 2
prokineticin receptor 2
NM_144944
1.7097
Csf1
colony stimulating factor 1 (macrophage)
NM_007778
1.70757
Mtmr10
myotubularin related protein 10
NM_172742
1.68499
Relb
NM_009046
1.68204
Ifitm3
avian reticuloendotheliosis viral (v-rel) oncogene
related homolog B
interferon induced transmembrane protein 3
NM_025378
1.67277
Npl
N-acetylneuraminate pyruvate lyase
NM_028749
1.67257
Ephx3
epoxide hydrolase 3
NM_001033163
1.67166
Tmem176a
transmembrane protein 176A
NM_025326
1.66412
Nrp1
neuropilin 1
NM_008737
1.6554
B2m
beta-2 microglobulin
NM_009735
1.65432
Aadacl2
arylacetamide deacetylase-like 2
NM_001128091
1.65394
Sdr16c5
Etv4
Development • Supplementary information
Development 143: doi:10.1242/dev.130898: Supplementary information
Serpinb5
serine (or cysteine) peptidase inhibitor, clade B,
member 5
serine (or cysteine) peptidase inhibitor, clade B,
member 6
malic enzyme 1, NADP(+)-dependent, cytosolic
NM_009257
1.65227
NM_011454
1.6513
NM_008615
1.6483
NM_001024139
1.64688
Sbsn
a disintegrin-like and metallopeptidase with
thrombospondin motifs 15
suprabasin
NM_172205
1.64486
Alox12e
arachidonate lipoxygenase, epidermal
NM_145684
1.64479
Tgfb1
transforming growth factor, beta 1
NM_011577
1.64403
Mest
mesoderm specific transcript
NM_008590
1.64183
Setbp1
SET binding protein 1
NM_053099
1.62694
Steap4
STEAP family member 4
NM_054098
1.62451
Serpinb3d
NM_201376
1.62108
Tmem176b
serine (or cysteine) peptidase inhibitor, clade B
(ovalbumin) member 3
transmembrane protein 176B
NM_023056
1.6186
Ikbke
inhibitor of kappaB kinase epsilon
NM_019777
1.61781
Elovl7
NM_029001
1.61718
Ankrd35
ELOVL family member 7, elongation of long chain fatty
acids
ankyrin repeat domain 35
NM_001081139
1.6135
Cxcl11
chemokine (C-X-C motif) ligand 11
NM_019494
1.60827
Ptges
prostaglandin E synthase
NM_022415
1.60778
Osmr
oncostatin M receptor
NM_011019
1.6042
Calml3
calmodulin-like 3
NM_027416
1.6038
Pthlh
parathyroid hormone-like peptide
NM_008970
1.60116
Lipm
lipase, family member M
NM_023903
1.60038
Orm1
orosomucoid 1
NM_008768
1.59549
Kcnip3
Kv channel interacting protein 3, calsenilin
NM_019789
1.58749
Phyhip
phytanoyl-CoA hydroxylase interacting protein
NM_145981
1.57769
Trim25
tripartite motif-containing 25
NM_009546
1.57537
Serpinb12
NM_027971
1.57423
Adra2b
serine (or cysteine) peptidase inhibitor, clade B
(ovalbumin) member 12
adrenergic receptor, alpha 2b
NM_009633
1.57349
Pla2g2f
phospholipase A2, group IIF
NM_012045
1.56977
Mapk4
mitogen-activated protein kinase 4
NM_172632
1.56745
Them5
thioesterase superfamily member 5
NM_025416
1.56526
Glul
glutamate-ammonia ligase (glutamine synthetase)
NM_008131
1.56162
Cspg4
chondroitin sulfate proteoglycan 4
NM_139001
1.55824
Rasgrp1
RAS guanyl releasing protein 1
NM_011246
1.55786
F3
coagulation factor III
NM_010171
1.55233
Serpinb6b
Me1
Adamts15
Development • Supplementary information
Development 143: doi:10.1242/dev.130898: Supplementary information
Ttc39b
tetratricopeptide repeat domain 39B
NM_027238
1.54678
Stard5
NM_023377
1.54597
Gsdmc
StAR-related lipid transfer (START) domain containing
5
gasdermin C
NM_031378
1.54584
Trex2
three prime repair exonuclease 2
NM_011907
1.54408
Clca5
chloride channel calcium activated 5
NM_178697
1.54023
Arhgef3
Rho guanine nucleotide exchange factor (GEF) 3
NM_027871
1.53812
Rdh12
retinol dehydrogenase 12
NM_030017
1.53806
Dapl1
death associated protein-like 1
NM_029723
1.53781
Serpinb7
NM_027548
1.53095
Parp12
serine (or cysteine) peptidase inhibitor, clade B,
member 7
poly (ADP-ribose) polymerase family, member 12
NM_172893
1.52898
Figf
c-fos induced growth factor
NM_010216
1.52603
Bnip3
BCL2/adenovirus E1B interacting protein 3
NM_009760
1.5244
Pdzk1ip1
PDZK1 interacting protein 1
NM_001164557
1.52419
Myb
myeloblastosis oncogene
NM_010848
1.52289
Lhx2
LIM homeobox protein 2
NM_010710
1.52144
Zdhhc2
zinc finger, DHHC domain containing 2
NM_178395
1.51928
Stra6
stimulated by retinoic acid gene 6
NM_009291
1.51604
Gsta1
glutathione S-transferase, alpha 1 (Ya)
NM_008181
1.5139
Acta2
actin, alpha 2, smooth muscle, aorta
NM_007392
1.51301
Car13
carbonic anhydrase 13
NM_024495
1.51048
Krt16
keratin 16
NM_008470
1.50953
Acsl1
acyl-CoA synthetase long-chain family member 1
NM_007981
1.50813
Gpm6b
glycoprotein m6b
NM_001177956
1.50714
Cxcl9
chemokine (C-X-C motif) ligand 9
NM_008599
1.5062
Tnip1
TNFAIP3 interacting protein 1
NM_021327
1.50449
Itpkb
inositol 1,4,5-trisphosphate 3-kinase B
NM_001081175
1.50267
Ptgs1
prostaglandin-endoperoxide synthase 1
NM_008969
1.50105
Sox9
SRY-box containing gene 9
NM_011448
1.50071
Acsl4
acyl-CoA synthetase long-chain family member 4
NM_207625
1.50053
Cald1
caldesmon 1
NM_145575
1.50041
b)
Upregulated in ∆N embryos:
Genes symbol
gene_assignment
Ref seq
Gm10304
predicted gene 10304
ENSMUST00000
94945
Fold
change
-3.26077
Development • Supplementary information
Development 143: doi:10.1242/dev.130898: Supplementary information
Mybpc1
myosin binding protein C, slow-type
NM_175418
-3.25459
Gm9911
predicted gene 9911
AK035883
-2.6811
Pcsk2
proprotein convertase subtilisin/kexin type 2
NM_008792
-2.5787
Igfbp3
insulin-like growth factor binding protein 3
NM_008343
-2.25564
Pisd-ps2
phosphatidylserine decarboxylase, pseudogene 2
NR_003519
-2.21286
St6galnac2
NM_009180
-2.20545
NM_080288
-2.13654
Unc5d
ST6 (Alpha-N-Acetyl-Neuraminyl-2,3-BetaGalactosyl-1,3)-N-Acetylgalactosaminide Alpha-2,6Sialyltransferase 2
engulfment and cell motility 1, ced-12 homolog (C.
elegans)
unc-5 homolog D (C. elegans)
NM_153135
-2.13157
Lrrn1
leucine rich repeat protein 1, neuronal
NM_008516
-2.10864
Ano4
anoctamin 4
NM_178773
-2.05626
Jun
Jun oncogene
NM_010591
-2.03491
Kcnh7
NM_133207
-1.98255
Cd68
potassium voltage-gated channel, subfamily H (eagrelated) member 7
CD68 antigen
NM_009853
-1.89433
Mir19b-1
microRNA 19b-1
NR_029815
-1.82456
Gria2
glutamate receptor, ionotropic, AMPA2 (alpha 2)
NM_013540
-1.78212
Lix1
limb expression 1 homolog (chicken)
NM_025681
-1.77782
Slc24a3
NM_053195
-1.76643
NM_012046
-1.74945
Cygb
solute carrier family 24 (sodium/potassium/calcium
exchanger) member 3
sporulation protein, meiosis-specific, SPO11
homolog
cytoglobin
NM_030206
-1.74346
Igf1
insulin-like growth factor 1
NM_010512
-1.74324
Npbwr1
neuropeptides B/W receptor 1
NM_010342
-1.73667
Scube1
signal peptide, CUB domain, EGF-like 1
NM_022723
-1.72514
Slc4a4
solute carrier family 4 (anion exchanger), member 4
NM_018760
-1.72296
1700001P01Rik
RIKEN cDNA 1700001P01 gene
NM_028156
-1.68043
Plcxd2
phosphatidylinositol-specific phospholipase C, X
domain containing 2
bone morphogenetic protein 2
NM_001134480
-1.67512
NM_007553
-1.66547
NM_001081173
-1.66022
B230325K18Rik
leucine-rich repeats and calponin homology (CH)
domain containing 2
RIKEN cDNA B230325K18 gene
-1.65577
AY512949
cDNA sequence AY512949
ENSMUST00000
079045
AY512949
Thsd7b
thrombospondin, type I, domain containing 7B
NM_172485
-1.64462
Lce6a
late cornified envelope 6A
NM_001166172
-1.63186
Pcdh10
protocadherin 10
NM_001098171
-1.63084
Elmo1
Spo11
Bmp2
Lrch2
-1.6508
Development • Supplementary information
Development 143: doi:10.1242/dev.130898: Supplementary information
Development 143: doi:10.1242/dev.130898: Supplementary information
Sprr2a1
small proline-rich protein 2A1
AY158986
-1.61029
Fam38b
family with sequence similarity 38, member B
NM_001039485
-1.6021
Mirlet7c-1
microRNA let7c-1
NR_029728
-1.59206
Cd96
CD96 antigen
NM_032465
-1.58805
Snora75
small nucleolar RNA, H/ACA box 75
NR_028478
-1.56597
Pcdh17
protocadherin 17
NM_001013753
-1.56052
Ripply3
ripply3 homolog (zebrafish)
NM_133229
-1.55827
Cdh6
cadherin 6
NM_007666
-1.55706
Dusp1
dual specificity phosphatase 1
NM_013642
-1.55033
Tagln3
transgelin 3
NM_019754
-1.54993
Col19a1
collagen, type XIX, alpha 1
NM_007733
-1.54267
Nkain2
Na+/K+ transporting ATPase interacting 2
NM_001013411
-1.52611
Gm12703
predicted gene 12703
-1.526
Baalc
brain and acute leukemia, cytoplasmic
ENSMUST00000
064804
NM_080640
Ica1
islet cell autoantigen 1
NM_010492
-1.51287
Igfbp2
insulin-like growth factor binding protein 2
NM_008342
-1.51232
Snhg1
small nucleolar RNA host gene (non-protein coding)
1
glutathione peroxidase 6
AK051045
-1.51117
NM_145451
-1.51012
TATA box binding protein (Tbp)-associated factor,
RNA polymerase I D
a disintegrin and metallopeptidase domain 1a
AK161656
-1.50123
NM_172126
-1.50059
Taf1d
Adam1a
Development • Supplementary information
Gpx6
-1.51608
Development 143: doi:10.1242/dev.130898: Supplementary information
Supplementary Table S3. Upper table: Number of NF-B binding sites and cross-species
conservation of all primary hair follicle placode-specific NF-B target genes that have been analysed
by qRT-PCR and ChIP (Lhx2, Sox9, Mmp9, Trps1) using an anti-p65 antibody. The right column
indicates whether a particular gene was also bound by NF-B subunits in Hodgkin’s lymphoma cell lines
(E. Kärgel and C. Scheidereit, unpublished). Previously unknown NF-B targets are marked in green (see
also http://www.bu.edu/nf-kb/gene-resources/target-genes/). Lower table: Cross-species conservation
and number of LHX2 binding sites in NF-B targets Nrp2 and Prokr2.
Number of potential
NF-B binding sites JASPER ( > 90%)
Cross species conservation - ECR
browser Dcode
Adamts3
Adamts15
Ascl4
3
6
0
Bcl3
Bmp2
5
2
Cd74
Cxcl9
Cxcl11
Dkk4
Dusp6
4
8
7
2
2
Etv4
Etv5
Fndc1
Foxi3
Frem1
Galnt6
Gli1
Krt17
Lhx2
Ltb
Madcam1
Mical2
Mmp9
Ncam1
Nrp2
Prokr2
Prss35
Ptch1
Ptch2
Pthlh
3
1
17
0
10
7
2
5
7
1
3
18
3
26
16
5
3
2
5
2
Binding sites are conserved in Muroidea
Binding sites are conserved in Muroidea
Binding sites are conserved up to
Metatheria
Binding sites are conserved in Mammals
Binding sites are conserved up to
Metatheria
Binding sites are conserved in Mammals
Binding sites are conserved in Mammals
Binding sites are conserved in Vertebrata
Binding sites are conserved up to
Metatheria
Binding sites are conserved in Muroidea
Binding sites are conserved in Mammals
Binding sites are conserved in Mammals
Binding sites are conserved in Mammals
Binding sites are conserved in Muroidea
Binding sites are conserved in Mammals
Binding site is conserved in Mammals
Binding sites are conserved in Muroidea
Binding sites are conserved in Muroidea
Binding sites are conserved in Mammals
Binding sites are conserved in Mammals
Binding sites are conserved in Mammals
Binding sites are conserved in Muroidea
Binding sites are conserved in Mammals
Binding sites are conserved in Mammals
ChIP peak of
NF-B
subunits in
Hodgkin
lymphoma
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Development • Supplementary information
Gene
symbol
Development 143: doi:10.1242/dev.130898: Supplementary information
Robo2
Scube1
Shh
Socs2
Sox9
Sox21
Srgap1
Tgfb1
Tnc
Tnf
Tnfaip3
Trps1
Tsku
Tspan18
Wif1
Wnt2b
Total
32
20
4
3
2
2
3
2
3
3
9
7
3
18
3
1
44 of 46 ~ 96%
Binding sites are conserved in Muroidea
Binding sites are conserved in Muroidea
Binding sites are conserved in Mammals
Binding sites are conserved in Mammals
Binding sites are conserved in Mammals
Binding sites are conserved in Vertebrata
Binding sites are conserved in Mammals
Binding sites are conserved in Muroidea
Binding sites are conserved in Mammals
Binding sites are conserved in Mammals
Binding sites are conserved up to Aves
Binding sites are conserved up to Aves
Binding sites are conserved in Mammals
Binding sites are conserved in Muroidea
Binding site is conserved in Mammals
Gene
symbol
Number of potential
LHX2 binding sites JASPER ( > 90%)
6
1
Cross species conservation - ECR
browser Dcode
Binding sites are conserved in Muroidea
Binding sites are not conserved
Development • Supplementary information
Nrp2
Prokr2
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
26 of 46 ~ 57%
Development 143: doi:10.1242/dev.130898: Supplementary information
Supplementary Table S4. List of genes specifically upregulated in the interfollicular epidermis (IFE),
but down-regulated by NF-B in hair follicle placodes at E14.5.
Genes
symbol
Pcsk2
Igfbp3
Igf1
Npbwr1
Lce6a
Ica1
Description
proprotein convertase
subtilisin/kexin type 2
insulin-like growth factor binding
protein 3
insulin-like growth factor 1
neuropeptides B/W receptor 1
late cornified envelope 6A
islet cell autoantigen 1
Ref seq
NM_008792
Fold change
(WT vs. ∆N)
-2.5787
Fold change (HF
vs IFE)
-2.04744
NM_008343
-2.25564
-1.70523
NM_010512
NM_010342
NM_001166172
NM_010492
-1.74324
-1.73667
-1.63186
-1.51287
-2.19222
-1.9776
-1.51564
-1.69649
Development • Supplementary information
Genes specifically upregulated in the interfollicular epidermis (IFE) and down-regulated by
NF-B in hair follicle placodes