Skip to main content Skip to navigation
Skinner Laboratory Genomic Data & R Code Files

Genomic Data –

Ben Maamar M, Nilsson E, Sadler-Riggleman I, Beck D, McCarrey J, Skinner MK (2018) Developmental Origins of Transgenerational Sperm DNA Methylation Epimutations Following Ancestral DDT Exposure (under review). GSE121585 (GEO in process and scheduled for release on January 19, 2019)

Skinner MK, Nilsson E, Sadler-Riggleman I, Beck D, McCarrey J (2018) Developmental Origins of Transgenerational Sperm DNA Methylation Epimutations Following Ancestral Vinclozolin Exposure (under review). GSE117995

Klukovich R, Nilsson E, Sadler-Riggleman I, Beck D, Xie Y, Yan W, Skinner MK (2018) Environmental Toxicant Induced Epigenetic Transgenerational Inheritance of Prostate Pathology and Stromal-Epithelial Cell Epigenome and Transcriptome Alterations: Ancestral Origins of Prostate Disease. (under review). GSE118447

Sadler-Riggleman I, Klukovich R, Nilsson E, Beck D, Xie Y, Yan W, Skinner MK (2018) Epigenetic Transgenerational Inheritance of Testis Pathology and Sertoli Cell Epimutations: Generational Origins of Male Infertility (under review). GSE118306

Nilsson E, Klukovich R, Sadler-Riggleman I, Beck D, Xie Y, Yan W, Skinner MK (2018) Environmental Toxicant Induced Epigenetic Transgenerational Inheritance of Ovarian Pathology and Granulosa Cell Epigenome and Transcriptome Alterations: Generational Origins of PCO and POI. Epigenetics 12:1-21. PMID: 30207508. GSE118381

Nilsson E, King SE, McBirney M, Kubsad D, Pappalardo M, Beck D, (2018) Vinclozolin induced epigenetic transgenerational inheritance of pathologies and sperm epimutation biomarkers for specific diseases. Plos One 13(8):1-29, e0202662. PMID: 30157260. GSE113785

King SE, McBirney M, Beck D, Sadler-Riggleman I, Nilsson E, Skinner MK (2018) Sperm Epimutation Biomarkers of Obesity and Pathologies following DDT Induced Epigenetic Transgenerational Inheritance of Disease (under review). GSE114032

Ben Maamar M, Sadler-Riggleman I, Beck D, Skinner MK (2018) Epigenetic Transgenerational Inheritance of Altered Sperm Histone Retention Sites. Scientific Reports 28;8(1):5308. PMID: 29593303. GSE106125

Ben Maamar M, Sadler-Riggleman I, Beck D, McBirney M, Nilsson E, Klukovich R, Xie Y, Tang C, Yan W, Skinner MK (2018) Alterations in sperm DNA Methylation, Non-Coding RNA expression, and histone retention mediate Vinclozolin induced epigenetic transgenerational inheritance of disease. Environmental Epigenetics 4(2):1-19, dvy101. PMID: 29732173. GSE111441

McBirney M, King SE, Pappalardo M, Houser E, Unkefer M, Nilsson E, Sadler-Riggleman I, Beck D, Winchester P, Skinner MK (2017) Atrazine Induced Epigenetic Transgenerational Inheritance of Disease, Lean Phenotype and Sperm Epimutation Pathology Biomarkers. Plos One 12(9):1-37, e0184306. PMID: 28931070. GSE98683

Carvan MJ, Kalluvila TA, Klingler RH, Larson JK, Pickens M, Mora-Zamorano FX, Connaughton VP, Sadler-Riggleman I, Beck D, Skinner MK (2017) Mercury-Induced Epigenetic Transgenerational Inheritance of Abnormal Neurobehavior is Correlated with Sperm Epimutations in Zebrafish. Plos One 12(5):1-26, e0176155. PMID: 28464002. GSE89144

Shnorhavorian M, Schwartz S, Sadler-Riggleman I, Beck D, Skinner MK (2017) Differential DNA Methylation Regions in Adult Human Sperm Following Adolescent Chemotherapy: Potential Epigenetic Inheritance . Plos One 12(2):1-18, e0170085. PMID:28146567. GSE85790

McNew S, Beck D, Sadler-Riggleman I, Knutie SA, Koop JAH, Clayton DH, Skinner MK (2017) Epigenetic variation between urban and rural populations of Darwin’s finches. BMC Evolutionary Biology 17:183. PMID: 28835203. GSE87825

Beck D, Sadler-Riggleman I, Skinner MK (2017) Generational Comparisons (F1 versus F3) of Vinclozolin Induced Epigenetic Transgenerational Inheritance of Sperm Differential DNA Methylation Regions (Epimutations) Using MeDIP-Seq. Environmental Epigenetics 3(3) pii: dvx016. PMID: 29147574. GSE96850

Thorson JM, Smithson M, Beck D, Sadler-Riggleman I, Nilsson E, Dybdahl M, Skinner MK (2017) Epigenetics and Adaptive Phenotypic Variation between Habitats in an Asexual Snail. Scientific Reports 7(1):14139. PMID: 29074962. GSE93836, GSE99911, GSE99912

Guillette L, Parrott B, Nilsson EE, Haque MM, Skinner MK (2016) Epigenetic programming alterations in alligators from environmentally contaminated lakes.  General and Comparative Endocrinology 1;238:4-12. PMID: 27080547. GSE82318

Skinner MK, Bhandari RK, Haque MM, Nilsson EE (2015) Environmentally Induced Epigenetic Transgenerational Inheritance of Altered SRY Genomic Binding During Gonadal Sex Determination. Environmental Epigenetics 1(1):1-10, dvv004. PMID: 27175298. GSE72469

Manikkam M, Haque MM, 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. PMID: 25057798. GSE58091

Skinner MK, Guerrero-Bosagna C, Haque MM, Knutie S, Koop J and Clayton D (2014) Epigenetics and the Evolution of Darwin’s Finches. Genome Biology and Evolution 24;6(8):1972-89.  PMID: 25062919. GSE58334

Skinner MK, Savenkova MI, Zhang B, Gore A, Crews D.  (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, Guerrero-Bosagna C, Haque MM, 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

Skinner MK, Guerrero-Bosagna C, Haque MM, Nilsson E, Bhandari R, and McCarrey JR. (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

Nilsson E, Zhang B, and Skinner MK. (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

Manikkam M, Guerrero-Bosagna C, Tracey R, Haque MM, and Skinner MK (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

Bhandari R, Schinke E, Haque MM, Sadler-Riggleman I, and Skinner MK.  (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.

Bhandari R, Haque MM, and Skinner MK. (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

Skinner MK, Manikkam M, Haque MM, Zhang B, Savenkova MI.  (2012) Epigenetic Transgenerational Inheritance of Somatic Transcriptomes and Epigenetic Control Regions. Genome Biology 3;13(10):R91. PMID: 23034163.  GSE35839

Nilsson E, Larsen G, Manikkam M, Guerrero-Bosagna C, Savenkova MI, Skinner MK. (2012) Environmentally Induced Epigenetic Transgenerational Inheritance of Ovarian Disease.  PLoS ONE  7(5):e36129. PMID:  22570695. GSE59278GSE33423, GSE59277 

Crews D, Gillette R, Manikkam M, Savenkova MI, Skinner MK.  (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

Nilsson EE, Schindler R, Savenkova MI, and Skinner MK. 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

Nilsson EE, Savenkova MI, Schindler R, Zhang B, Schadt EE, and Skinner MK.  (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 MI, 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
SlidingWindowCluster.R

 

MeDIP-Seq –

Lab Analysis Code – Git Hub