Growth factor, augmenter of liver regeneration
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1 Supplemental Table 1: Human and mouse PC1 sequence equivalencies Human Mouse Domain Clinical significance; Score* PolyPhen prediction; PSIC score difference C210G C210G WSC Highly likely pathogenic; 15 Probably damaging; V690D V685D Between C-Lectin Highly likely pathogenic; 13 Probably damaging; & PKD-2 G1166S G1160S PKD-5 Likely pathogenic; 10 Possibly damaging; R2089 C2085R PKD-15 No report Possibly damaging; L2816P L2811P REJ Likely pathogenic; 6 Probably damaging; L3048H L3040H GPS No report Probably damaging; Y4109X Y4100X COOH-terminus No report ND R4213X R4204X COOH-terminus No report ND R4228X R4218X COOH-terminus Definitely pathogenic ND *From: Highly likely pathogenic: >11 Likely pathogenic: 5-10 Indeterminate: <4 Definitely pathogenic: nonsense mutation Supplemental Table 2: Genes contained in BAC RPCI22-287A3 Gene Symbol Gene name Traf7** TNF receptor-associated factor 7 Rab26 RAB26, member RAS oncogene family Pkd1 Polycystic kidney disease gene 1 Tsc2 tuberous sclerosis 2 Nthl 1 Nth endonuclease III-like 1 Slc9a3r2 Solute carrier family 9 (sodium/hydron exchanger), member 3 regulator Npw Neuropeptide W Zfp598 Zinc finger protein 598 Syngr3 Synaptogrin3 Gfer** Growth factor, augmenter of liver regeneration *Genes are list in order from the centromeric telomeric orientation on the chromosome. **Partial genes. Supplemental Table 3: Expression levels of PC1 in Pkd1 F/H -BAC transgenic mouse lines. Transgenic line # Tg248 Tg276 Tg8 Tg14 qpcr copy number Relative protein expression* Functional rescue yes yes yes yes * Relative protein expression is normalized to relative expression from transgenic line #14. ND, not determine.
2 Supplemental Table 4: transgenic lines. Functional rescue of embryonic lethality of Pkd1 / mice by the Pkd1 F/H -BAC Transgenic line # Pkd1 +/+ ;Pkd1 F/H -BAC Pkd1 +/ ;Pkd1 F/H -BAC Pkd1 / ;Pkd1 F/H -BAC Tg248 2 (22%) 3 (33%) 4 (45%) Tg276 8 (20%) 24 (60%) 8 (20%) Tg8 7 (35%) 7 (35%) 6 (30%) Tg14 5 (28%) 9 (50%) 4 (22%) Totals 37 (27%) 66 (48%) 34 (25%) Supplemental Table 5: Failure of functional rescue of embryonic lethality of Pkd1 / mice by the Pkd1 L3040H -BAC transgenic lines. Transgenic line qpcr copy Pkd1 +/+ ;Pkd1 L3040H Pkd1 +/ ;Pkd1 L3040H Pkd1 / ;Pkd1 L3040H # number Tg (25%) 39 (75%) 0 (0%) Tg7 3 9 (41%) 13 (59%) 0 (0%) Tg9 1 5 (33%) 10 (67%) 0 (0%) Totals N/A 27 (30%) 62 (70%) 0 (0%) N/A: not applicable.
3 Supplemental Figure 1 Alternate projections from a 3D view assembled from z-stack images showing abundant expression of the respective Pc1 pathogenic missense mutations, Pc1-C210G and Pc1-V685G, in the cell bodies (green) and absence from cilia (red). These are the same mutant variants presented in Fig. 3D and 3E, respectively. Scale bar, 8 µm.
4 Supplemental Figure 2 Strategy of the PCR genotyping endogenous and BAC alleles of Pkd1. (A) Schematic representation of the WT (Pkd1), null (Pkd1 ) and FLAG-tagged BAC (Pkd1 F/H -BAC) alleles showing location of genotyping primers and respective product sizes. (B) Representative PCR genotyping for mice with the indicated genotypes.
5 Supplemental Figure 3 Functional rescue of Pkd1 / mice by the Pkd1 F/H -BAC transgene. Kidney, liver and pancreas tissue sections stained with hematoxylin and eosin from 6 month old mice with genotypes Pkd1 / ;Pkd1 F/H -BAC (Tg248), Pkd1 / ;Pkd1 F/H -BAC (Tg276), and wild type (WT). The respective Pkd1 F/H -BAC transgenes completely rescue the Pkd1 / phenotype. Size bars, 500 µm.
6 Supplemental Figure 4 GPS cleavage-deficient Pc1 L3040H interacts with PC2. PC1 L3040H does not undergo GPS cleavage (top left panel) but interacts with PC2 as indicated by co-immunoprecipitation (right panels). COOH-terminal truncated PC2 L703X does not interact with PC1 and does not co-ip with it. Co-expression of wild type PC2 increases expression of PC1-CTF (top left panel), whereas co-expression with PC2L 703X does not. PC2-myc, PC2 L703X - myc, PC1 and PC1 L3040H were transiently expressed in COS7 cells as indicated. Lysates were IP using antimyc. PC1 and PC1 L3040H were detected by immunoblotting with anti-ha antibodies while PC2 and PC2 L703X were detected using YCB9 anti-pc2 antisera.
7 Supplemental Figure 5 Proteasomal Inhibition does not restore Pc1-CTF levels in the absence of Pc2. (A) SF4 Pkd2 fl/fl ;Pkd1 F/H -BAC cells (+/+) and SF3A Pkd2 / ;Pkd1 F/H -BAC cells ( / ) with and without treatment with carfilzomib (100 nm for 16 hours) followed by immunoblotting with anti-ha to detect Pc1-CTF. Carfilzomib treatment did not increase in the steady state level of Pc1-CTF. (B) Effective inhibition of proteasome function in SF3A cells was documented by increased Hif1α expression in carfilzomib-treated cells compared with DMSO treated controls. Tubulin serves as loading control.
8 Supplemental Figure 6 Loss of Pc1 does not affect steady state levels of Pc2. Whole tissue lysates of E16.5 mouse embryos with the indicated genotypes show no effect on Pc2 expression. PC2-HA is transfected cell lysate.
Figure S1. Figure S2. Figure S3 HB Anti-FSP27 (COOH-terminal peptide) Ab. Anti-GST-FSP27(45-127) Ab.
/ 36B4 mrna ratio Figure S1 * 2. 1.6 1.2.8 *.4 control TNFα BRL49653 Figure S2 Su bw AT p iw Anti- (COOH-terminal peptide) Ab Blot : Anti-GST-(45-127) Ab β-actin Figure S3 HB2 HW AT BA T Figure S4 A TAG
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DOI:.38/ncb327 a b Sequence coverage (%) 4 3 2 IP: -GFP isoform IP: GFP IP: -GFP IP: GFP Sequence coverage (%) 4 3 2 IP: -GFP IP: GFP 33 52 58 isoform 2 33 49 47 IP: Control IP: Peptide Sequence Start
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Supporting Information
Supporting Information Fujii et al. 10.1073/pnas.1217563110 A Human Cen chromosome 4q ART3 NUP54 SCARB2 FAM47E CCDC8 Tel B Bac clones RP11-54D17 RP11-628A4 Exon 1 2 34 5 6 7 8 9 10 11 12 5 3 PCR region
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TRANSGENIC ANIMALS. -transient transfection of cells -stable transfection of cells. - Two methods to produce transgenic animals:
TRANSGENIC ANIMALS -transient transfection of cells -stable transfection of cells - Two methods to produce transgenic animals: 1- DNA microinjection - random insertion 2- embryonic stem cell-mediated gene
Supplementary Fig. 1
a FL (1-2266) NL (1-1190) CL (1191-2266) HA-ICE1: - HA-ICE1: - - - FLAG-ICE2: + + + + FLAG-ELL: + + + + + + IP: anti-ha FLAG-ICE2 HA-ICE1-FL HA-ICE1-NL HA-ICE1-CL FLAG-ICE2 b IP: anti-ha FL (1-2266) NL
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Pei et al. Supplementary Figure S1
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A H. sapiens 204 TKLQTS--ERANKLAAPSVSH VSPRKNPSVVIKPEACS-PQFGKTSFPTKESFSANMS LP 259 B. taurus 201 TKLQSS--ERANKLAVPTVSH VSPRKSPSVVIKPEACS-PQFGKPSFPTKESFSANKS LP 257 M. musculus 204 TKSQSN--GRTNKPAAPSVSH
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Supplemental Table 1: Sequences of real time PCR primers. Primers were intronspanning
Symbol Accession Number Sense-primer (5-3 ) Antisense-primer (5-3 ) T a C ACTB NM_001101.3 CCAGAGGCGTACAGGGATAG CCAACCGCGAGAAGATGA 57 HSD3B2 NM_000198.3 CTTGGACAAGGCCTTCAGAC TCAAGTACAGTCAGCTTGGTCCT 60
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Supporting Information He et al. 10.1073/pnas.1116302108 SI Methods Cell Culture. Mouse J774A.1 and RAW 264.7 macrophages were obtained from ATCC and were cultured in MEM supplemented with 10% FS (Sigma)
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T H E J O U R N A L O F C E L L B I O L O G Y Supplemental material Rainero et al., http://www.jcb.org/cgi/content/full/jcb.201109112/dc1 Figure S1. The expression of DGK- is reduced upon transfection
Nature Structural & Molecular Biology: doi: /nsmb.3308
Supplementary Figure 1 Analysis of CED-3 autoactivation and CED-4-induced CED-3 activation. (a) Repeat experiments of Fig. 1a. (b) Repeat experiments of Fig. 1b. (c) Quantitative analysis of three independent
Supplemental Material
Supplemental Material 1 Figure S1. Phylogenetic analysis of Cep72 and Lrrc36, comparative localization of Cep72 and Lrrc36 and Cep72 antibody characterization (A) Phylogenetic alignment of Cep72 and Lrrc36
Revised: RG-RV2 by Fukuhara et al.
Supplemental Figure 1 The generation of Spns2 conditional knockout mice. (A) Schematic representation of the wild type Spns2 locus (Spns2 + ), the targeted allele, the floxed allele (Spns2 f ) and the
JCB. Supplemental material THE JOURNAL OF CELL BIOLOGY. Kimura et al.,
Supplemental material JCB Kimura et al., http://www.jcb.org/cgi/content/full/jcb.201503023/dc1 THE JOURNAL OF CELL BIOLOGY Figure S1. TRIMs regulate IFN-γ induced autophagy. (A and B) HC image analysis
Supplemental Information
Supplemental Information Intrinsic protein-protein interaction mediated and chaperonin assisted sequential assembly of a stable Bardet Biedl syndome protein complex, the BBSome * Qihong Zhang 1#, Dahai
Supplemental Data. Sethi et al. (2014). Plant Cell /tpc
Supplemental Data Supplemental Figure 1. MYC2 Binds to the E-box but not the E1-box of the MPK6 Promoter. (A) E1-box and E-box (wild type) containing MPK6 promoter fragment. The region shown in red denotes
Nature Biotechnology: doi: /nbt Supplementary Figure 1. In vitro validation of OTC sgrnas and donor template.
Supplementary Figure 1 In vitro validation of OTC sgrnas and donor template. (a) In vitro validation of sgrnas targeted to OTC in the MC57G mouse cell line by transient transfection followed by 4-day puromycin
T H E J O U R N A L O F C E L L B I O L O G Y
Supplemental material Kunduri et al., http://www.jcb.org/cgi/content/full/jcb.201405020/dc1 T H E J O U R N A L O F C E L L B I O L O G Y Figure S1. Subcellular localization and interactions of PAPLA1.
Supplemental data. Zhao et al. (2009). The Wuschel-related homeobox gene WOX11 is required to activate shoot-borne crown root development in rice.
Supplemental data. Zhao et al. (2009). The Wuschel-related homeobox gene WOX11 is required to activate shoot-borne crown root development in rice. A B Supplemental Figure 1. Expression of WOX11p-GUS WOX11-GFP
(phosphatase tensin) domain is shown in dark gray, the FH1 domain in black, and the
Supplemental Figure 1. Predicted Domain Organization of the AFH14 Protein. (A) Schematic representation of the predicted domain organization of AFH14. The PTEN (phosphatase tensin) domain is shown in dark
Supplementary Materials for
www.sciencetranslationalmedicine.org/cgi/content/full/8/347/347ra94/d Supplementary Materials for n mirn-mediated therapy for S6 blocks IRES-driven translation of the N second cistron Yu Miyazaki, Xiaofei
Supplementary Information
Supplementary Information Supplementary Figure 1: Over-expression of CD300f in NIH3T3 cells enhances their capacity to phagocytize AC. (a) NIH3T3 cells were stably transduced by EV, CD300f WT or CD300f
Supplementary Figure 1. Confirmation of sirna in PC3 and H1299 cells PC3 (a) and H1299 (b) cells were transfected with sirna oligonucleotides
Supplementary Figure 1. Confirmation of sirna in PC3 and H1299 cells PC3 (a) and H1299 (b) cells were transfected with sirna oligonucleotides targeting RCP (SMARTPool (RCP) or two individual oligos (RCP#1
Supplemental Data. Cui et al. (2012). Plant Cell /tpc a b c d. Stem UBC32 ACTIN
A Root Stem Leaf Flower Silique Senescence leaf B a b c d UBC32 ACTIN C * Supplemental Figure 1. Expression Pattern and Protein Sequence of UBC32 Homologues in Yeast, Human, and Arabidopsis. (A) Expression