List of Supplementary Figures and Tables Supplementary Material, Fig. S1: Confirmation that YY1 and NLRP7 directly interact in HEK293T cells. Supplementary.

Slides:



Advertisements
Similar presentations
Supplementary Fig. 1. Transcriptome analysis of MENX-associated pituitary adenomas and and comparison with human studies. Control samples from wild-type.
Advertisements

25 A hMLH1 B Acetylated H3 Enrichment SW480 RKO Position from +1 BBII ++-- SW480 BIBI ++-- RKO C hMLH1 GAPDH Ab D Methyl-H3-K4 enrichment Position.
Figure S1. RNA-seq results for caveolin-1 (Cav1). Upper panel: UCSC genome browser view. Lower panel: quantification o f Cav1 expression based on RNA-seq.
Ct log DNA ( pmol) P1P2 Supplementary Fig. S1 Standard curve of the PCR amplification efficiency of transcripts.
Marker (%) Normal EPCs Mean ± SM (%) MMD EPCs Mean ± SM (%) CD ± ± 6.8 KDR27.3 ± ± 8.90 CD ± ± 3.93 CD ±
Adipose PancreasAorta MuscleHeart Liver LungKidney Testis Spleen Brian 18S p55 γ p55 α Figure S1 Tissue distribution of p55 . (A) Representative RT-PCR.
1A IP/ Input Figure 1: E47 is present on tRNA genes 1B IgG TFIIB E47 Brf1 WB: Brf1 Input IP A) IP/Input enrichment of E47 at 6 active tRNA genes and one.
Supplementary Figures Fig. 1 Transcript levels of Tissue Factor, PAR-1 and PAR-2 Expression if TF, PAR-1 and PAR-2 was analyzed in unstimulated HUVECs,
CpG hypermethylation Data from literature RESULT: Genes that are hypermethylated at CpG islands in cancer cells (HCT- 116 cell line) are NOT highly.
Supplementary Figure S1 FPKM ESRP1ESRP2 normaltumor Supplementary Figure S1. ESRP1 and ESRP2 mRNA expression in 65 normal kidney samples and 474 ccRCC.
Supplementary Fig. 1. RT-PCR showed that tumor tissues have elevated Mst1 mRNA levels in most of the HCC patients tested. GAPDH RT-PCR products were shown.
(b) Relative Abundance K P D L R y2y2 y3y3 y4y4 b2b2 b4b4 b3b3 y1y1 b1b1.V R. Relative Abundance y2y2 y3y3 y4y4 b2b2 b4b4 b3b3 y1y1 b1b1.V R. K ME2 P D.
NOVEL BRCA2-INTERACTING PROTEIN BJ-HCC-20A INHIBITS THE INDUCTION OF APOPTOSIS IN RESPONSE TO DNA DAMAGE Go Tomiyoshi, Akira Nakanishi, Katsuya Takenaka,
Wu et al., Supplementary Fig 1 Supplementary Figure 1: The depletion of BRG1 in HeLa cells has no effect on cell proliferation. Sh- empty vector was used.
Date of download: 9/19/2016 Copyright © 2016 American Medical Association. All rights reserved. From: Germline Epigenetic Regulation of KILLIN in Cowden.
Supplementary Figure S4
A B C D ** CpG-free Luc -7,200 -5,900 e2piNOS-luc -4,900 e1piNOS-luc
Volume 7, Issue 5, Pages (November 2016)
Fig. S1. Work flow diagram..
Figure 1. DNMT3A interacts with the histone deiminase PADI4
Fig. 2. Development and validation of shRNAs for SOCE components
Hypoxia increases IL-32 expression in an HIF1α-dependent manner.
Volume 18, Issue 2, Pages (February 2010)
Suppl. Figure 3 A H1975 Atg7 shRNA 3 MOI Atg7 shRNA 6 MOI
Induction of Pluripotent Stem Cells from Mouse Embryonic and Adult Fibroblast Cultures by Defined Factors  Kazutoshi Takahashi, Shinya Yamanaka  Cell 
A Requirement for ZAK Kinase Activity in Canonical TGF-β Signaling
Volume 81, Issue 1, Pages (January 2012)
Epigenetic mechanisms silence a disintegrin and metalloprotease 33 expression in bronchial epithelial cells  Youwen Yang, PhD, Hans Michael Haitchi, MD,
GLUT3 is a direct target of TCF4/β‐catenin
Volume 55, Issue 1, Pages (July 2014)
Volume 21, Issue 9, Pages (November 2017)
A Requirement for ZAK Kinase Activity in Canonical TGF-β Signaling
Epigenetic Inhibition of Nuclear Receptor Small Heterodimer Partner Is Associated With and Regulates Hepatocellular Carcinoma Growth  Nan He, Kyungtae.
Volume 47, Issue 2, Pages (July 2012)
Volume 76, Issue 1, Pages (July 2009)
Yu-Hsin Chiu, Jennifer Y. Lee, Lewis C. Cantley  Molecular Cell 
Expression and regulation of MD-2s.
Volume 144, Issue 5, Pages e4 (May 2013)
Volume 133, Issue 6, Pages (December 2007)
Differential DNA Methylation as a Tool for Noninvasive Prenatal Diagnosis (NIPD) of X Chromosome Aneuploidies  Floriana Della Ragione, Paola Mastrovito,
Assessing loss of imprint methylation in sperm from subfertile men using novel methylation polymerase chain reaction Luminex analysis  Akiko Sato, M.E.,
Volume 13, Issue 2, Pages (October 2015)
Daniel Wolf, Stephen P. Goff  Cell 
Volume 7, Issue 5, Pages (November 2016)
Quantitative analysis of DNA methylation of imprinted genes in single human blastocysts by pyrosequencing  John Huntriss, Ph.D., Kathryn Woodfine, Ph.D.,
Volume 44, Issue 3, Pages (November 2011)
Volume 135, Issue 3, Pages e3 (September 2008)
Volume 25, Issue 1, Pages (April 2013)
Volume 18, Issue 2, Pages (February 2010)
Supplementary Figure 1 IP: IgG HA 3HA-E2F1: cIAP1: wt K
Andrew W Snowden, Philip D Gregory, Casey C Case, Carl O Pabo 
Volume 5, Issue 5, Pages (November 2015)
HDAC1 positively regulates the abundance of miRNAs.
Supplementary Fig. S1 BCL2 5’flanking ctrl siRNA luc
ADAR Regulates RNA Editing, Transcript Stability, and Gene Expression
Volume 15, Issue 11, Pages (June 2016)
Validation of cell types and functional validation of KAP1 knockout
Insulin-Like Growth Factor-Binding Protein 7 Regulates Keratinocyte Proliferation, Differentiation and Apoptosis  Janna Nousbeck, Ofer Sarig, Nili Avidan,
Volume 20, Issue 4, Pages (April 2011)
Volume 13, Issue 6, Pages (November 2015)
Jakub Tolar, Lily Xia, Megan J. Riddle, Chris J. Lees, Cindy R
LncRNA TRERNA1 Function as an Enhancer of SNAI1 Promotes Gastric Cancer Metastasis by Regulating Epithelial-Mesenchymal Transition  Huazhang Wu, Ying.
Volume 27, Issue 6, Pages (September 2007)
Short Telomeres in ESCs Lead to Unstable Differentiation
Fig. 1. Coilin interaction with the telomerase complex protein dyskerin is mediated by hTR. Coilin interaction with the telomerase complex protein dyskerin.
Volume 14, Issue 3, Pages (March 2014)
Molecular Therapy - Nucleic Acids
(A) Relative expression levels of the top most down-regulated genes in LATS2L breast tumors (TCGA-BRCA dataset, see Fig 1) in the panel of breast cancer.
Chk1 and 14‐3‐3 proteins inhibit atypical E2Fs to prevent a permanent cell cycle arrest Experimental procedures of the SILAC assay to identify binding.
Volume 55, Issue 1, Pages (July 2014)
Presentation transcript:

List of Supplementary Figures and Tables Supplementary Material, Fig. S1: Confirmation that YY1 and NLRP7 directly interact in HEK293T cells. Supplementary Material, Fig. S2: NLRP7 expression levels in human cell lines Supplementary Material, Fig. S3: NLRP7 (panel A) and NLRP2 (panel B) expression levels in BeWo cells before and after NLRP7 knockdown. Supplementary Material, Fig. S4: (A) Bisulfite validation of regions with altered methylation in undifferentiated hESC cultures. (B) FBXO4 expression in BeWo cells. (C) ZFP42 expression in BeWo cells. Supplementary Material, Fig. S5: Methylation differences at imprinted DMRs. Supplementary Material, Fig. S6: Methylation levels at ZFP42 in HM tissue. Supplementary Material, Table S1: List of 864 probes with significantly altered methylation at F>50 (Excel file) Supplementary Material, Table S2: List of 234 gene regions with altered methylation at F>5 (Excel file) Supplementary Material, Table S3: Statistics of identified probes with significantly altered methylation

Supplementary Material, Fig. S1 : YY1 and NLRP7 directly interact in HEK293T cells. N-terminal Myc-tagged YY1 and N-terminal V5-tagged NLRP7 were co-expressed in HEK293T cells. Compared to immunoprecipitation (IP) with IgG (negative control), IP with anti-V5 followed by immunoblotting (IB) with anti-Myc (upper panel), as well as immunoprecipitation with anti-NLRP7, followed by immunoblotting with anti-YY1 (lower panel) confirmed that NLRP7 binds to YY1. IP V5IP IgGInput IB: Myc IP NLRP7IP IgGInput IB: YY1

Supplementary Material, Fig. S2: NLRP7 expression levels in various human cell lines. Quantitative RT-PCR was performed to compare levels of NLRP7 between various cell lines. Expression was standardized to GAPDH expression and ΔΔCt method was used to quantify relative expression. The BeWo choriocarcinoma cell line has the highest levels, followed by H9 human embryonic stem cells (H9 hESC) which have ~30% NLRP7 expression compared to BeWo cells, and HEK293T cells, which have undetectable levels.

AB Supplementary Material, Fig. S3: NLRP7 (panel a) and NLRP2 (panel b) expression levels in BeWo cells before and after NLRP7 knockdown. Cells were transiently transfected with Dharmacon ON-TARGET plus siRNA Pool (siNLRP7 KD ) or the Non-Targeting Pool (siNLRP7 NTP ). Quantitative RT-PCR was performed to amplify NLRP7 mRNA (a) or NLRP2 mRNA (b). Expression was standardized to GAPDH expression and the ΔΔCt method was used to quantify relative expression compared to untransfected cells (Mock). The siRNA pool efficiently knocked down NLRP7 expression by ~85%, but did not affect NLRP2 expression.

CpG Clones H9 hESC shNLRP7 SC shNLRP7 KD Supplementary Material, Fig. S4: A) Bisulfite validation of regions with altered methylation in undifferentiated hESC cultures. B) FBXO4 expression in BeWo cells. Expression level determined by quantitative real-time PCR of FBXO4 is not different in cells transfected with the siRNA pool compared to cells transfected with the scrambled siRNA and mock transfected cells C) ZFP42 expression in BeWo cells. Expression level determined by quantitative real-time PCR of ZFP42 is also not different in cells transfected with the siRNA pool compared to cells transfected with the scrambled siRNA and mock transfected cells A B C

Supplementary Material, Fig. S5: Methylation differences at imprinted DMRs. Results at A) PEG3, B) KCNQ1OT1, C) H19 and D) SNRPN are shown for undifferentiated and differentiated shNLRP7 KD, shNLRP7 SC, and untransduced hES cells showing no difference in DNA methylation at any of these loci. Each is shown as a graph with the methylation levels on the Y-axis and the individual probes in the region listed on the X-axis. A B C D

TP#1 TP#2 POC#1POC#2POC#3 Pt#1 Pt#2 Pt#3 Supplementary Material, Fig. S6: Methylation levels at ZFP42 in HM tissue. Bisulfite sequencing at ZFP42 in A) Term placenta B) Products of conception, C) Corresponding patients with HM. No difference in DNA methylation is noted at ZFP42 when comparing term placenta with HM tissue. A B C