Comparison of Gene Expression Profiles Between Dental Pulp and Periodontal Ligament Tissues in Humans
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Genazzani-2003-Calcineurin And
Edinburgh Research Explorer Calcineurin controls the expression of numerous genes in cerebellar granule cells Citation for published version: Kramer, D, Fresu, L, Ashby, DS, Freeman, TC & Genazzani, AA 2003, 'Calcineurin controls the expression of numerous genes in cerebellar granule cells', Molecular and Cellular Neuroscience, vol. 23, no. 2, pp. 325- 30. Link: Link to publication record in Edinburgh Research Explorer Document Version: Publisher's PDF, also known as Version of record Published In: Molecular and Cellular Neuroscience Publisher Rights Statement: © 2003 Elsevier Science (USA) General rights Copyright for the publications made accessible via the Edinburgh Research Explorer is retained by the author(s) and / or other copyright owners and it is a condition of accessing these publications that users recognise and abide by the legal requirements associated with these rights. Take down policy The University of Edinburgh has made every reasonable effort to ensure that Edinburgh Research Explorer content complies with UK legislation. If you believe that the public display of this file breaches copyright please contact [email protected] providing details, and we will remove access to the work immediately and investigate your claim. Download date: 28. Sep. 2021 Molecular and Cellular Neuroscience 23 (2003) 325–330 www.elsevier.com/locate/ymcne Calcineurin controls the expression of numerous genes in cerebellar granule cells Dana Kramer,a Luigia Fresu,b Dominique S. Ashby,a Tom C. Freeman,c and Armando A. Genazzania,* a Department of Pharmacology, Tennis Court Road, Cambridge, CB2 1PD, UK b Department of Pharmacology, Gynaecology and Obstetrics, University of Sassari, Italy c Microarray Group, MRC HGMP-RC, Wellcome Trust Genome Campus, Hinxton, CB10 1SB, UK Received 31 October 2002; revised 7 January 2003; accepted 20 January 2003 Abstract The Ca2ϩ/calmodulin-dependent phosphatase calcineurin plays a crucial role in gene expression in different cell types such as T-lymphocytes, cardiac myocytes, and smooth muscle cells. -
Viewed Under 23 (B) Or 203 (C) fi M M Male Cko Mice, and Largely Unaffected Magni Cation; Scale Bars, 500 M (B) and 50 M (C)
BRIEF COMMUNICATION www.jasn.org Renal Fanconi Syndrome and Hypophosphatemic Rickets in the Absence of Xenotropic and Polytropic Retroviral Receptor in the Nephron Camille Ansermet,* Matthias B. Moor,* Gabriel Centeno,* Muriel Auberson,* † † ‡ Dorothy Zhang Hu, Roland Baron, Svetlana Nikolaeva,* Barbara Haenzi,* | Natalya Katanaeva,* Ivan Gautschi,* Vladimir Katanaev,*§ Samuel Rotman, Robert Koesters,¶ †† Laurent Schild,* Sylvain Pradervand,** Olivier Bonny,* and Dmitri Firsov* BRIEF COMMUNICATION *Department of Pharmacology and Toxicology and **Genomic Technologies Facility, University of Lausanne, Lausanne, Switzerland; †Department of Oral Medicine, Infection, and Immunity, Harvard School of Dental Medicine, Boston, Massachusetts; ‡Institute of Evolutionary Physiology and Biochemistry, St. Petersburg, Russia; §School of Biomedicine, Far Eastern Federal University, Vladivostok, Russia; |Services of Pathology and ††Nephrology, Department of Medicine, University Hospital of Lausanne, Lausanne, Switzerland; and ¶Université Pierre et Marie Curie, Paris, France ABSTRACT Tight control of extracellular and intracellular inorganic phosphate (Pi) levels is crit- leaves.4 Most recently, Legati et al. have ical to most biochemical and physiologic processes. Urinary Pi is freely filtered at the shown an association between genetic kidney glomerulus and is reabsorbed in the renal tubule by the action of the apical polymorphisms in Xpr1 and primary fa- sodium-dependent phosphate transporters, NaPi-IIa/NaPi-IIc/Pit2. However, the milial brain calcification disorder.5 How- molecular identity of the protein(s) participating in the basolateral Pi efflux remains ever, the role of XPR1 in the maintenance unknown. Evidence has suggested that xenotropic and polytropic retroviral recep- of Pi homeostasis remains unknown. Here, tor 1 (XPR1) might be involved in this process. Here, we show that conditional in- we addressed this issue in mice deficient for activation of Xpr1 in the renal tubule in mice resulted in impaired renal Pi Xpr1 in the nephron. -
Supplementary Table 1: Adhesion Genes Data Set
Supplementary Table 1: Adhesion genes data set PROBE Entrez Gene ID Celera Gene ID Gene_Symbol Gene_Name 160832 1 hCG201364.3 A1BG alpha-1-B glycoprotein 223658 1 hCG201364.3 A1BG alpha-1-B glycoprotein 212988 102 hCG40040.3 ADAM10 ADAM metallopeptidase domain 10 133411 4185 hCG28232.2 ADAM11 ADAM metallopeptidase domain 11 110695 8038 hCG40937.4 ADAM12 ADAM metallopeptidase domain 12 (meltrin alpha) 195222 8038 hCG40937.4 ADAM12 ADAM metallopeptidase domain 12 (meltrin alpha) 165344 8751 hCG20021.3 ADAM15 ADAM metallopeptidase domain 15 (metargidin) 189065 6868 null ADAM17 ADAM metallopeptidase domain 17 (tumor necrosis factor, alpha, converting enzyme) 108119 8728 hCG15398.4 ADAM19 ADAM metallopeptidase domain 19 (meltrin beta) 117763 8748 hCG20675.3 ADAM20 ADAM metallopeptidase domain 20 126448 8747 hCG1785634.2 ADAM21 ADAM metallopeptidase domain 21 208981 8747 hCG1785634.2|hCG2042897 ADAM21 ADAM metallopeptidase domain 21 180903 53616 hCG17212.4 ADAM22 ADAM metallopeptidase domain 22 177272 8745 hCG1811623.1 ADAM23 ADAM metallopeptidase domain 23 102384 10863 hCG1818505.1 ADAM28 ADAM metallopeptidase domain 28 119968 11086 hCG1786734.2 ADAM29 ADAM metallopeptidase domain 29 205542 11085 hCG1997196.1 ADAM30 ADAM metallopeptidase domain 30 148417 80332 hCG39255.4 ADAM33 ADAM metallopeptidase domain 33 140492 8756 hCG1789002.2 ADAM7 ADAM metallopeptidase domain 7 122603 101 hCG1816947.1 ADAM8 ADAM metallopeptidase domain 8 183965 8754 hCG1996391 ADAM9 ADAM metallopeptidase domain 9 (meltrin gamma) 129974 27299 hCG15447.3 ADAMDEC1 ADAM-like, -
Supplementary Table S4. FGA Co-Expressed Gene List in LUAD
Supplementary Table S4. FGA co-expressed gene list in LUAD tumors Symbol R Locus Description FGG 0.919 4q28 fibrinogen gamma chain FGL1 0.635 8p22 fibrinogen-like 1 SLC7A2 0.536 8p22 solute carrier family 7 (cationic amino acid transporter, y+ system), member 2 DUSP4 0.521 8p12-p11 dual specificity phosphatase 4 HAL 0.51 12q22-q24.1histidine ammonia-lyase PDE4D 0.499 5q12 phosphodiesterase 4D, cAMP-specific FURIN 0.497 15q26.1 furin (paired basic amino acid cleaving enzyme) CPS1 0.49 2q35 carbamoyl-phosphate synthase 1, mitochondrial TESC 0.478 12q24.22 tescalcin INHA 0.465 2q35 inhibin, alpha S100P 0.461 4p16 S100 calcium binding protein P VPS37A 0.447 8p22 vacuolar protein sorting 37 homolog A (S. cerevisiae) SLC16A14 0.447 2q36.3 solute carrier family 16, member 14 PPARGC1A 0.443 4p15.1 peroxisome proliferator-activated receptor gamma, coactivator 1 alpha SIK1 0.435 21q22.3 salt-inducible kinase 1 IRS2 0.434 13q34 insulin receptor substrate 2 RND1 0.433 12q12 Rho family GTPase 1 HGD 0.433 3q13.33 homogentisate 1,2-dioxygenase PTP4A1 0.432 6q12 protein tyrosine phosphatase type IVA, member 1 C8orf4 0.428 8p11.2 chromosome 8 open reading frame 4 DDC 0.427 7p12.2 dopa decarboxylase (aromatic L-amino acid decarboxylase) TACC2 0.427 10q26 transforming, acidic coiled-coil containing protein 2 MUC13 0.422 3q21.2 mucin 13, cell surface associated C5 0.412 9q33-q34 complement component 5 NR4A2 0.412 2q22-q23 nuclear receptor subfamily 4, group A, member 2 EYS 0.411 6q12 eyes shut homolog (Drosophila) GPX2 0.406 14q24.1 glutathione peroxidase -
Transcriptomic Uniqueness and Commonality of the Ion Channels and Transporters in the Four Heart Chambers Sanda Iacobas1, Bogdan Amuzescu2 & Dumitru A
www.nature.com/scientificreports OPEN Transcriptomic uniqueness and commonality of the ion channels and transporters in the four heart chambers Sanda Iacobas1, Bogdan Amuzescu2 & Dumitru A. Iacobas3,4* Myocardium transcriptomes of left and right atria and ventricles from four adult male C57Bl/6j mice were profled with Agilent microarrays to identify the diferences responsible for the distinct functional roles of the four heart chambers. Female mice were not investigated owing to their transcriptome dependence on the estrous cycle phase. Out of the quantifed 16,886 unigenes, 15.76% on the left side and 16.5% on the right side exhibited diferential expression between the atrium and the ventricle, while 5.8% of genes were diferently expressed between the two atria and only 1.2% between the two ventricles. The study revealed also chamber diferences in gene expression control and coordination. We analyzed ion channels and transporters, and genes within the cardiac muscle contraction, oxidative phosphorylation, glycolysis/gluconeogenesis, calcium and adrenergic signaling pathways. Interestingly, while expression of Ank2 oscillates in phase with all 27 quantifed binding partners in the left ventricle, the percentage of in-phase oscillating partners of Ank2 is 15% and 37% in the left and right atria and 74% in the right ventricle. The analysis indicated high interventricular synchrony of the ion channels expressions and the substantially lower synchrony between the two atria and between the atrium and the ventricle from the same side. Starting with crocodilians, the heart pumps the blood through the pulmonary circulation and the systemic cir- culation by the coordinated rhythmic contractions of its upper lef and right atria (LA, RA) and lower lef and right ventricles (LV, RV). -
Integrin Alpha-5 Silencing Leads to Myofibroblastic Differentiation In
TAJ0010.1177/2040622320936023Therapeutic Advances in Chronic DiseaseGE Shochet 936023research-article20202020 Therapeutic Advances in Chronic Disease Original Article Ther Adv Chronic Dis Integrin alpha-5 silencing leads to 2020, Vol. 11: 1–12 DOI:https://doi.org/10.1177/2040622320936023 10.1177/ myofibroblastic differentiation in IPF- 2040622320936023https://doi.org/10.1177/2040622320936023 © The Author(s), 2020. Article reuse guidelines: derived human lung fibroblasts sagepub.com/journals- permissions Gali Epstein Shochet* , Elizabetha Brook*, Becky Bardenstein-Wald, Hanna Grobe, Evgeny Edelstein, Lilach Israeli-Shani and David Shitrit Abstract Background and objective: The term ‘fibroblast’ covers a heterogeneous cell population in idiopathic pulmonary fibrosis (IPF). The fibroblasts are considered as main effector cells, because they promote disease progression by releasing exaggerated amounts of extracellular matrix proteins and modifying cell microenvironment. As IPF-derived human lung fibroblasts (IPF-HLFs) were shown to express higher levels of integrin alpha-5 (ITGA5) than normal derived HLFs (N-HLFs), we explored the importance of ITGA5 to IPF progression. Methods: IPF-HLF and N-HLF primary cultures were established. ITGA5 was silenced by specific small interfering RNA (siRNA)s and its effects on cell phenotype (e.g. cell number, size, cell death, migration) and gene expression (e.g. RNA sequencing, quantitative polymerase chain reaction [qPCR], western blot and immunofluorescence) were tested. Specific integrin expression was evaluated in IPF patient formalin-fixed paraffin embedded sections by immunohistochemistry (IHC). Results: ITGA5-silencing resulted in reduced IPF-HLF proliferation rates and cell migration (p < 0.05), as well as elevated cell death. transforming growth factor beta (TGF-β) targets (e.g. Fibronectin (FN1), Matrix metalloproteinase 2 (MMP2), TGFB1) were surprisingly elevated following ITGA5 silencing (p < 0.05). -
An Atlas of Chromatin Accessibility in the Adult Human Brain
Downloaded from genome.cshlp.org on October 4, 2021 - Published by Cold Spring Harbor Laboratory Press Resource An atlas of chromatin accessibility in the adult human brain John F. Fullard,1,2,3,12 Mads E. Hauberg,1,2,4,5,6,12 Jaroslav Bendl,1,2,3 Gabor Egervari,1,2,7 Maria-Daniela Cirnaru,8 Sarah M. Reach,3 Jan Motl,9 Michelle E. Ehrlich,3,8,10 Yasmin L. Hurd,1,2,7 and Panos Roussos1,2,3,11 1Department of Psychiatry, 2Friedman Brain Institute, 3Department of Genetics and Genomic Science and Institute for Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA; 4iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, 8000 Aarhus C, Denmark; 5Department of Biomedicine, 6Centre for Integrative Sequencing (iSEQ), Aarhus University, 8000 Aarhus C, Denmark; 7Department of Neuroscience, 8Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA; 9Department of Theoretical Computer Science, Faculty of Information Technology, Czech Technical University in Prague, Prague 1600, Czech Republic; 10Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA; 11Mental Illness Research, Education, and Clinical Center, James J. Peters VA Medical Center, Bronx, New York 10468, USA Most common genetic risk variants associated with neuropsychiatric disease are noncoding and are thought to exert their effects by disrupting the function of cis regulatory elements (CREs), including promoters and enhancers. Within each cell, chromatin is arranged in specific patterns to expose the repertoire of CREs required for optimal spatiotemporal regulation of gene expression. -
Molecular Processes During Fat Cell Development Revealed by Gene
Open Access Research2005HackletVolume al. 6, Issue 13, Article R108 Molecular processes during fat cell development revealed by gene comment expression profiling and functional annotation Hubert Hackl¤*, Thomas Rainer Burkard¤*†, Alexander Sturn*, Renee Rubio‡, Alexander Schleiffer†, Sun Tian†, John Quackenbush‡, Frank Eisenhaber† and Zlatko Trajanoski* * Addresses: Institute for Genomics and Bioinformatics and Christian Doppler Laboratory for Genomics and Bioinformatics, Graz University of reviews Technology, Petersgasse 14, 8010 Graz, Austria. †Research Institute of Molecular Pathology, Dr Bohr-Gasse 7, 1030 Vienna, Austria. ‡Dana- Farber Cancer Institute, Department of Biostatistics and Computational Biology, 44 Binney Street, Boston, MA 02115. ¤ These authors contributed equally to this work. Correspondence: Zlatko Trajanoski. E-mail: [email protected] Published: 19 December 2005 Received: 21 July 2005 reports Revised: 23 August 2005 Genome Biology 2005, 6:R108 (doi:10.1186/gb-2005-6-13-r108) Accepted: 8 November 2005 The electronic version of this article is the complete one and can be found online at http://genomebiology.com/2005/6/13/R108 © 2005 Hackl et al.; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which deposited research permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Gene-expression<p>In-depthadipocytecell development.</p> cells bioinformatics were during combined fat-cell analyses with development de of novo expressed functional sequence annotation tags fo andund mapping to be differentially onto known expres pathwayssed during to generate differentiation a molecular of 3 atlasT3-L1 of pre- fat- Abstract Background: Large-scale transcription profiling of cell models and model organisms can identify novel molecular components involved in fat cell development. -
Potent Lipolytic Activity of Lactoferrin in Mature Adipocytes
Biosci. Biotechnol. Biochem., 77 (3), 566–571, 2013 Potent Lipolytic Activity of Lactoferrin in Mature Adipocytes y Tomoji ONO,1;2; Chikako FUJISAKI,1 Yasuharu ISHIHARA,1 Keiko IKOMA,1;2 Satoru MORISHITA,1;3 Michiaki MURAKOSHI,1;4 Keikichi SUGIYAMA,1;5 Hisanori KATO,3 Kazuo MIYASHITA,6 Toshihide YOSHIDA,4;7 and Hoyoku NISHINO4;5 1Research and Development Headquarters, Lion Corporation, 100 Tajima, Odawara, Kanagawa 256-0811, Japan 2Department of Supramolecular Biology, Graduate School of Nanobioscience, Yokohama City University, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan 3Food for Life, Organization for Interdisciplinary Research Projects, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan 4Kyoto Prefectural University of Medicine, Kawaramachi-Hirokoji, Kamigyou-ku, Kyoto 602-8566, Japan 5Research Organization of Science and Engineering, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga 525-8577, Japan 6Department of Marine Bioresources Chemistry, Faculty of Fisheries Sciences, Hokkaido University, 3-1-1 Minatocho, Hakodate, Hokkaido 041-8611, Japan 7Kyoto City Hospital, 1-2 Higashi-takada-cho, Mibu, Nakagyou-ku, Kyoto 604-8845, Japan Received October 22, 2012; Accepted November 26, 2012; Online Publication, March 7, 2013 [doi:10.1271/bbb.120817] Lactoferrin (LF) is a multifunctional glycoprotein resistance, high blood pressure, and dyslipidemia. To found in mammalian milk. We have shown in a previous prevent progression of metabolic syndrome, lifestyle clinical study that enteric-coated bovine LF tablets habits must be improved to achieve a balance between decreased visceral fat accumulation. To address the energy intake and consumption. In addition, the use of underlying mechanism, we conducted in vitro studies specific food factors as helpful supplements is attracting and revealed the anti-adipogenic action of LF in pre- increasing attention. -
Integrin and Gene Network Analysis Reveals That ITGA5 and ITGB1 Are Prognostic in Non-Small-Cell Lung Cancer
Journal name: OncoTargets and Therapy Article Designation: Original Research Year: 2016 Volume: 9 OncoTargets and Therapy Dovepress Running head verso: Zheng et al Running head recto: ITGA5 and ITGB1 are prognostic in NSCLC open access to scientific and medical research DOI: http://dx.doi.org/10.2147/OTT.S91796 Open Access Full Text Article ORIGINAL RESEARCH Integrin and gene network analysis reveals that ITGA5 and ITGB1 are prognostic in non-small-cell lung cancer Weiqi Zheng Background: Integrin expression has been identified as a prognostic factor in non-small-cell Caihui Jiang lung cancer (NSCLC). This study was aimed at determining the predictive ability of integrins Ruifeng Li and associated genes identified within the molecular network. Patients and methods: A total of 959 patients with NSCLC from The Cancer Genome Atlas Department of Radiation Oncology, Guangqian Hospital, Quanzhou, Fujian, cohorts were enrolled in this study. The expression profile of integrins and related genes were People’s Republic of China obtained from The Cancer Genome Atlas RNAseq database. Clinicopathological characteristics, including age, sex, smoking history, stage, histological subtype, neoadjuvant therapy, radiation therapy, and overall survival (OS), were collected. Cox proportional hazards regression models as well as Kaplan–Meier curves were used to assess the relative factors. Results: In the univariate Cox regression model, ITGA1, ITGA5, ITGA6, ITGB1, ITGB4, and ITGA11 were predictive of NSCLC prognosis. After adjusting for clinical factors, ITGA5 (odds ratio =1.17, 95% confidence interval: 1.05–1.31) andITGB1 (odds ratio =1.31, 95% confidence interval: 1.10–1.55) remained statistically significant. In the gene cluster network analysis, PLAUR, ILK, SPP1, PXN, and CD9, all associated with ITGA5 and ITGB1, were identified as independent predictive factors of OS in NSCLC. -
Supplementary Table 2: Infection-Sensitive Genes
Supplementary Table 2: Infection-Sensitive Genes Supplementary Table 2: Upregulated with Adenoviral Infection (pages 1 - 7)- genes that were significant by ANOVA as well as significantly increased in control compared to both 'infected control' (Ad-LacZ) and 'calcineurin infected' (Ad-aCaN). Downregulated with Adenoviral Infection (pages 7 - 13) as above except for direction of change. Columns: Probe Set- Affymetrix probe set identifier for RG-U34A microarray, Symbol and Title- annotated information for above probe set (annotation downloaded June, 2004), ANOVA- p-value for 1-way Analysis of Variance, Uninfected, Ad-LacZ and Ad- aCaN- mean ± SEM expression for uninfected control, adenovirus mediated LacZ treated control, and adenovirus mediated calcineurin treated cultures respectively. Upregulated with Adenoviral Infection Probe Set Symbol Title ANOVA Uninfected Ad-LacZ Ad-aCaN Z48444cds_at Adam10 a disintegrin and metalloprotease domain 10 0.00001 837 ± 31 1107 ± 24 1028 ± 29 L26986_at Adcy8 adenylyl cyclase 8 0.00028 146 ± 12 252 ± 21 272 ± 21 U94340_at Adprt ADP-ribosyltransferase 1 0.00695 2096 ± 100 2783 ± 177 2586 ± 118 U01914_at Akap8 A kinase anchor protein 8 0.00080 993 ± 44 1194 ± 65 1316 ± 44 AB008538_at Alcam activated leukocyte cell adhesion molecule 0.01012 2775 ± 136 3580 ± 216 3429 ± 155 M34176_s_at Ap2b1 adaptor-related protein complex 2, beta 1 subunit 0.01389 2408 ± 199 2947 ± 143 3071 ± 116 D44495_s_at Apex1 apurinic/apyrimidinic endonuclease 1 0.00089 4959 ± 185 5816 ± 202 6057 ± 158 U16245_at Aqp5 aquaporin 5 0.02710 -
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BRIEF COMMUNICATION www.jasn.org Comparison of Glomerular and Podocyte mRNA Profiles in Streptozotocin-Induced Diabetes † † † ‡ † Jia Fu,* Chengguo Wei, Kyung Lee, Weijia Zhang, Wu He, Peter Chuang, Zhihong Liu,* † and John Cijiang He § *National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China; †Division of Nephrology, Department of Medicine, ‡Flow Cytometry Shared Resource Facility, Icahn School of Medicine at Mount Sinai, New York; §Renal Program, James J. Peters VA Medical Center at Bronx, New York. ABSTRACT Evaluating the mRNA profile of podocytes in the diabetic kidney may indicate STZ induction alone.10 In order to spe- genes involved in the pathogenesis of diabetic nephropathy. To determine if the cifically label and isolate podoctyes, we 2 2 podocyte-specific gene information contained in mRNA profiles of the whole crossed the eNOS / mice with the IRG glomerulus of the diabetic kidney accurately reflects gene expression in the isolated mice11 that ubiquitously express a red 2/2 podocytes, we crossed Nos3 IRG mice with podocin-rtTA and TetON-Cre mice fluorescent protein prior to Cre-mediated for enhanced green fluorescent protein labeling of podocytes before diabetic injury. recombination and an enhanced green Diabetes was induced by streptozotocin, and mRNA profiles of isolated glomeruli fluorescent protein (EGFP) following re- and sorted podocytes from diabetic and control mice were examined 10 weeks combination. These mice were further later. Expression of podocyte-specific markers in glomeruli was downregulated in bred with podocin-rtTA and TetON-Cre diabetic mice compared with controls. However, expression of these markers was (LC1) transgenic mice for inducible not altered in sorted podocytes from diabetic mice.