Skinner Laboratory

Genomic Data and R Code Files

Genomic Data -

Manikkam M, Haque M, Guerrero-Bosagna C, Nilsson EE, Skinner MK (2014) Pesticide Methoxychlor Promotes the Epigenetic Transgenerational Inheritance of Adult-Onset Disease through the Female Germline. PLoS ONE 9(7)e102091. GSE58091

Michael K. Skinner, Carlos Guerrero-Bosagna, Md. Haque, Sarah Knutie, Jennifer Koop and Dale Clayton (2014) Epigenetics and the Evolution of Darwin’s Finches. Genome Biology and Evolution 24;6(8):1972-89.  GSE58334

Michael K. Skinner, Marina Savenkova, Bin Zhang, Andrea Gore, David Crews.  (2014) Gene Bionetworks Involved in the Epigenetic Transgenerational Inheritance of Mate Preference: Environmental Epigenetics and Evolutionary Biology. BMC Genomics 16;15:377. PMID: 24885959.  GSE33830

Tracey R, Manikkam M, Guerrero-Bosagna C, Skinner MK. (2013) Hydrocarbons (jet fuel JP-8) induce epigenetic transgenerational inheritance of obesity, reproductive disease and sperm epimutations. Reprod Toxicol. Apr;36:104-16. PMID: 23453003.  GSE59553

Manikkam M, Tracey R, Guerrero-Bosagna C, Skinner MK. (2013) Plastics derived endocrine disruptors (BPA, DEHP and DBP) induce epigenetic transgenerational inheritance of obesity, reproductive disease and sperm epimutations. PLoS One. 8(1):e55387. PMID: 23359474. GSE59555

Skinner MK, Haque CG, Nilsson E, Bhandari R, McCarrey JR. (2013) Environmentally induced transgenerational epigenetic reprogramming of primordial germ cells and the subsequent germ line. PLoS One.  15;8(7):e66318. PMID: 23869203. GSE59511, GSE43559, GSE59510

Michael K Skinner, Carlos Guerrero-Bosagna, Md. M. Haque, Eric Nilsson, Ramji Bhandari and John McCarrey. (2013) Environmentally Induced Transgenerational Epigenetic Reprogramming of Primordial Cells and Subsequent Germline. PLoS ONE 2013 15;8(7):e66318. PMID: 23869203. GSE43559

Guerrero-Bosagna C, Savenkova M, Haque MM, Nilsson E, Skinner MK. (2013) Environmentally Induced Epigenetic Transgenerational Inheritance of Altered Sertoli Cell Transcriptome and Epigenome: Molecular Etiology of Male Infertility. PLoS One. 8(3):e59922. PMID: 23555832.  GSE59110, GSE41173, GSE59109

Eric Nilsson, Bin Zhang and Michael K. Skinner. (2013) Gene Bionetworks that Regulate Ovarian Primordial Follicle Assembly.  BMC Genomics. 23;14:496. PMID: 23875758. GSE43464

Manikkam M, Tracey R, Guerrero-Bosagna C, Skinner MK. (2012) Dioxin (TCDD) induces epigenetic transgenerational inheritance of adult onset disease and sperm epimutations. PLoS One. 7(9):e46249.  PMID:  23049995.  GSE59552

Manikkam M, Tracey R, Guerrero-Bosagna C, Skinner MK. (2012) Pesticide and insect repellent mixture (permethrin and DEET) induces epigenetic transgenerational inheritance of disease and sperm epimutations. Reprod Toxicol. 34(4):708-19.  PMID: 22975477. GSE59554

Mohan Manikkam, Carlos Guerrero-Bosagna, Rebecca Tracey, Md. M. Haque and Michael K. Skinner (2012) Transgenerational Actions of Environmental Compounds on Reproductive Disease and Identification of Epigenetic Biomarkers of Ancestral Exposures. PLoS ONE 7(2):e31901. PMID: 22389676. GSE57693

Ramji K. Bhandari, Ellyn Schinke, Md. M. Haque, Ingrid Sadler-Riggleman and Michael K. Skinner.  (2012) SRY Induced TCF21 Genome-wide Targets and Cascade of bHLH Factors During Sertoli Cell Differentiation and Male Sex Determination in Rats. Biol Reprod 6;87(6):131. PMID: 23034159.

Ramji K. Bhandari, Md. M. Haque and Michael K. Skinner. (2012) Global Genome Analysis of the Downstream Targets of Testis Determining Factor SRY and SOX9.  PLoS ONE 7(9):e43380. PMID: 22984422. GSE63854, GSE63855GSE63856, GSM1558510, GSM1558511, GSM1558512

Michael K. Skinner, Mohan Manikkam, Md. M. Haque, Bin Zhang, Marina Savenkova.  (2012) Epigenetic Transgenerational Inheritance of Somatic Transcriptomes and Epigenetic Control Regions. Genome Biology 3;13(10):R91. PMID: 23034163.  GSE35839

Eric Nilsson, Ginger Larsen, Mohan Manikkam, Carlos Guerrero-Bosagna, Marina Savenkova, Michael K. Skinner. (2012) Environmentally Induced Epigenetic Transgenerational Inheritance of Ovarian Disease.  PLoS ONE  7(5):e36129. PMID:  22570695. GSE59278GSE33423, GSE59277 

David Crews, Ross Gillette, Mohan Manikkam, Marina I. Savenkova, Michael K. Skinner.  (2012) Epigenetic Transgenerational Alterations to Stress Response in Brain Gene Networks and Behaviour.  PNAS 5;109(23):9143-8.  PMID:  22615374.  GSE26737

Bhandari RK, Sadler-Riggleman I, Clement TM, Skinner MK.  (2011) basic helix-loop-helix transcription factor Tcf21 is downstream target of male sex determining gene Sry.  PLoS One. 6(5):e19935.  PMID: 21637323.  GSE24666

Eric E. Nilsson, Ryan Schindler, Marina I. Savenkova and Michael K. Skinner. Inhibitory Actions of Anti-Müllerian Hormone (AMH) on Ovarian Primordial Follicle Assembly.  PLoS One. 2011;6(5):e20087.  PMID: 21637711. GSE25629

Schindler R, Nilsson E, Skinner MK. (2010) Induction of ovarian primordial follicle assembly by connective tissue growth factor CTGF. PLoS One. 24;5(9):e12979. PMID: 20886044. GSE22096

Eric E. Nilsson, Marina I. Savenkova, Ryan Schindler, Bin Zhang, Eric E. Schadt and Michael K. Skinner.  (2010) Gene Bionetwork Analysis of Ovarian Primordial Follicle Development. PLoS One. 16;5(7):e11637. PMID: 20661288. GSE20324

Clement TM, Savenkova MI, Settles M, Anway MD, Skinner MK. (2010) Alterations in the developing testis transcriptome following embryonic vinclozolin exposure. Reprod Toxicol. 30(3):353-64. PMID: 20566332. GSE20245

Nilsson E, Dole G, Skinner MK. (2009) Neurotrophin NT3 promotes ovarian primordial to primary follicle transition. Reproduction. 138(4):697-707.  PMID: 19584175. GSE20358

Stevens JD, Roalson EH, Skinner MK. (2008) Phylogenetic and expression analysis of the basic helix-loop-helix transcription factor gene family: genomic approach to cellular differentiation. Differentiation. 76(9):1006-22.  PMID: 18557763. GSE20259

Skinner M, Anway M, Savenkova M, Gore AC, Crews D (2008) Transgenerational epigenetic programming of the brain transcriptome and anxiety behavior. PLoS ONE 3(11):e3745. PMID: 19015723 - GSE14269

Anway MD, Rekow SS, Skinner MK. (2008) Transgenerational epigenetic programming of the embryonic testis transcriptome.  Genomics. 91(1):30-40. PMID: 18042343 - GSE10919

Anway MD, Skinner MK. (2008) Transgenerational effects of the endocrine disruptor vinclozolin on the prostate transcriptome and adult onset disease. Prostate. 1;68(5):517-29. PMID: 18220299 - GSE11842

Dole G, Nilsson EE, Skinner MK. (2008) Glial-derived neurotrophic factor promotes ovarian primordial follicle development and cell-cell interactions during folliculogenesis. Reproduction. 135(5):671-82.
PMID: 18304989  - GSE11133

Skinner MK, Schmidt M, Savenkova MI, Sadler-Riggleman I, Nilsson EE. (2008) Regulation of granulosa and theca cell transcriptomes during ovarian antral follicle development. Mol Reprod Dev. 75(9):1457-72. PMID: 18288646 - GSE11495

Clement TM, Anway MD, Uzumcu M, Skinner MK. (2007) Regulation of the gonadal transcriptome during sex determination and testis morphogenesis: comparative candidate genes. Reproduction. 134(3):455-72. PMID: 17709564- GSE10558

Nilsson E, Rogers N, Skinner MK. (2007) Actions of anti-Mullerian hormone on the ovarian transcriptome to inhibit primordial to primary follicle transition. Reproduction. 2007 Aug;134(2):209-21. PMID: 17660231- GSE10557

Nilsson EE, Stanfield J, Skinner MK. (2006) Interactions between progesterone and tumor necrosis factor-alpha in the regulation of primordial follicle assembly. Reproduction. 132(6):877-86. PMID: 17127748 - The data discussed in this publication have been deposited in NCBIs Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo/) and are accessible through GEO Series accession number GSE8238

Kezele PR, Ague JM, Nilsson E, Skinner MK. (2005) Alterations in the ovarian transcriptome during primordial follicle assembly and development. Biol Reprod 2005 Jan;72(1):241-55. PMID: 15371273 - The data discussed in this publication have been deposited in NCBIs Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo/) and are accessible through GEO Series accession number GSE9300

Small CL, Shima JE, Uzumcu M, Skinner MK et al. (2005) Profiling gene expression during the differentiation and development of the murine embryonic gonad. Biol Reprod. 72(2):492-501. PMID: 15496517 -- The data discussed in this publication have been deposited in NCBIs Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo/) and are accessible through GEO Series accession number GSE6916, GSE1359, GSE1358, GSE6881 and GSE6882 

Meachem SJ, Ruwanpura SM, Ziolkowski J, Ague JM et al. (2005) Developmentally distinct in vivo effects of FSH on proliferation and apoptosis during testis maturation. J Endocrinol. 186(3):429-46. PMID: 16135663 - The data discussed in this publication have been deposited in NCBIs Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo/) and are accessible through GEO Series accession number GSE10293

 

R-Code Files -

ChIP-Chip Analysis

MeDIP-Chip Analysis

ComputeDiff.R

Median300Bp.R

Normalize.R

readNimblegen.R

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