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Skinner Laboratory Genomic Data & R Code Files

Genomic Data –

Thompson R, Beck D, Nilsson EE, Ben Maamar M, Shnorhavorian M, Skinner MK (2022) Examination of Generational Impacts of Adolescent Chemotherapy: Ifosfamide and Potential for Epigenetic Inheritance. iScience (conditionally accepted)  GSE217141 is currently private and is scheduled to be released on Nov 30, 2022.

Duncan GE, Avery A, Ben Maamar M, Nilsson EE, Beck D, Skinner MK. (2022) Epigenome-wide Association Study for Physical Activity and Physiological Parameters in Discordant Monozygotic Twins. (submitted)  GSE216387 is currently private and is scheduled to be released on Dec 01, 2022.

Ben Maamar M, Wang Y, Nilsson EE, Beck D, Yan W, Skinner MK. (2022) Transgenerational Sperm DMRs Escape Methylation Erasure in Embryonic Epigenetic Inheritance. (Submitted).  GSE211135 – is currently private and is scheduled to be released on Nov 10, 2022.

Kaefer M, Rink R, Misseri R, Winchester P, Proctor C, Ben Maamar M, Beck D, Nilsson E, Skinner MK (2022) Role of Epigenetics in the Etiology of Hypospadias through Penile DNA Methylation Alterations. (submitted) GEO # GSE200681

Winchester P, Nilsson E, Beck D, Skinner MK. (2022) Preterm birth buccal cell epigenetic biomarkers to facilitate preventative medicine. Scientific Reports 12, 3361. PMID: 35232984, GSE194227

Beck, D, Nilsson E, Ben Maamar M, Skinner MK. (2022) Environmental Induced Transgenerational Inheritance Impacts Systems Epigenetics in Disease Etiology. Scientific Reports. 2022 Apr 19;12(1):5452.  PMID: 35440735.  GSE98683, GSE155922, GSE157539, GSE158254, GSE158086, GSE163412, GSE152678, and GSE198452

Beck D, Ben Maamar M, Skinner MK (2022) Genome-wide CpG Density and DNA Methylation Analysis Methods (MeDIP, RRBS, and GWBS) Comparisons. Epigenetics. 2021 May 17(5):518-530. PMID: 33975521. (GEO # GSE99129, GSE121585, GSE89144, GSE71567, GSE145887, GSE157417, GSE85790, GSE134362, GSE105766, GSE104221, SRP076725, GSE99272, GSE98064, GSE100470, SRS1788540, SRS1793712)

Garrido N, Cruz F, Rivera Egea R, Simon C, Sadler-Riggleman I, Beck D, Nilsson E, Skinner MK (2021) Sperm DNA Methylation Epimutation Biomarker for Paternal Offspring Autism Susceptibility. Clinical Epigenetics 13:6. PMID: 33413568, GSE157417

Thorson JLM, Beck D, Ben Maamar M, Nilsson E, Skinner MK (2021) Ancestral Plastics Exposure Induces Transgenerational Disease Specific Sperm Epigenome-Wide Association Biomarkers. Environmental Epigenetics 7(1):dvaa023, (pp. 1-13). PMID: 33841921, GSE163412

Beck D, Ben Maamar M, Skinner MK (2021) Integration of Sperm ncRNA Directed DNA Methylation and DNA Methylation Directed Histone Retention in Epigenetic Transgenerational Inheritance. Epigenetics and Chromatin 14(1):6. PMID: 33436057, GSE109775 and GSE106125

Ben Maamar M, Beck D, Sadler-Riggleman I, Nilsson E, McCarrey JR, Skinner MK (2021) Developmental Alterations in DNA Methylation During Gametogenesis from Primordial Germ Cells to Sperm. iScience 25(2):103786. PMID: 35146397, GSE117995 & GSE151458

Kelley JL, Tobler M, Beck D, Barts N, Sadler-Riggleman I, Quackenbush CR, Rodriguez LA, Skinner MK (2021) Epigenetic Inheritance of DNA Methylation Changes in Fish Living in Hydrogen Sulfide-rich Springs. Proc Natl Acad Sci U S A. 2021 Jun 29;118(26):e2014929118. PMID: 34185679, GSE157730

Nilsson E, Sadler-Riggleman I, Beck D, Skinner MK (2021) Differential DNA Methylation in Somatic and Sperm Cells of Hatchery versus Wild (Natural-Origin) Steelhead Trout Populations Phenotypic Variation. Environ Epigenet. 2021 May 19;7(1):dvab002. PMID: 34040807 , GSE145887

Ben Maamar M, Beck D, Thorson JLM, Nilsson E, Kubsad D, Skinner MK (2020) Epigenome-wide Association Study for Glyphosate Induced Transgenerational Sperm DNA Methylation and Histone Retention Epigenetic Biomarkers for Disease. Epigenetics. 2021 Oct;16(10):1150-1167. PMID: 33296237, GSE152678

Thorson JLM, Beck D, Ben Maamar M, Nilsson E, McBirney M, Skinner MK (2020) Epigenome-Wide Association Study for Atrazine Induced Transgenerational DNA Methylation and Histone Retention Sperm Epigenetic Biomarkers for Disease. PLoS One. 2020 Dec 16;15(12):e0239380. PMID: 33326428,  GSE156530

Ben Maamar M, Nilsson E, Thorson JLM, Beck D, Skinner MK (2020) Epigenome-Wide Association Study for Transgenerational Disease Sperm Epimutation Biomarkers following Ancestral Exposure to Jet Fuel Hydrocarbons. Reprod Toxicol 2020;S0890-6238(20)30198-2. PMID: 32905848,  GSE155922

Ben Maamar M, Nilsson E, Thorson JLM, Beck D, Skinner MK (2021) Transgenerational Disease Specific Epigenetic Sperm Biomarkers after Ancestral Exposure to Dioxin. Environmental Research 2020 Oct 8:110279. PMID: 33039529,  GSE157539

Nilsson E, Thorson JLM, Ben Maamar M, Beck D, Skinner MK (2020) Epigenome-Wide Association Study (EWAS) Identifies Transgenerational Disease Biomarkers in Sperm Following Ancestral Exposure to the Pesticide Methoxychlor. Environmental Epigenetics, 6(1):dvaa020. PMID: 33391823,  GSE158086

Thorson JLM, Beck D, Ben Maamar M, Nilsson E, McBirney M, Skinner MK (2020) Epigenome-Wide Association Study for Pesticide (Permethrin and DEET) Induced DNA Methylation Epimutation Biomarkers for Specific Transgenerational Disease. Environmental Health (2020) 19:109. pp1-17. PMID: 33148267,  GSE158254

Ben Maamar M, King S, Nilsson E, Sadler-Riggleman I, Beck D, Skinner MK (2020) Epigenetic Transgenerational Inheritance of Parent-of-Origin Allelic Transmission of Outcross Pathology and Sperm Epimutations. Developmental Biology, 458(1):106-119. PMID: 31682807. GSE130258

Ben Maamar M, Beck D, Nilsson E, McCarrey JR, Skinner MK (2020) Developmental Origins of Transgenerational Sperm Histone Retention Following Ancestral Exposures. Developmental Biology, 465(1):31-45. GSE137963

Smithson M, Thorson JLM, Sadler-Riggleman I, Beck D, Dybdahl M, Skinner MK (2020) Between-generation phenotypic and epigenetic stability in a clonal snail suggests transgenerational plasticity. Genome Biol Evol, 12(9):1604-1615. GSE99912 and GSE144681

King SE, Nilsson E, Beck D, Skinner MK (2019) Adipocyte Epigenetic Alterations and Potential Therapeutic Targets in Transgenerationally Inherited Lean and Obese Phenotypes Following Ancestral Exposures. Adipocyte 8(1):362-378. PMID:31755359. GSE137536

Luján S, Caroppo E, Niederberger C, Arce JC, Sadler-Riggleman I, Beck D, Nilsson E, Skinner MK (2019) Sperm DNA Methylation Epimutation Biomarkers for Male Infertility and FSH Therapeutic Responsiveness.  Scientific Reports 9:16786. PMID: 31727924. GSE135825

Thorson JLM, Smithson M, Sadler-Riggleman I, Beck D, Dybdahl M, Skinner MK (2019) Regional Epigenetic Variation in Asexual Snail Populations among Different Urban and Rural Lakes. Environmental Epigenetics 5(4):1-12, dvz020. PMID: 31723440. GSE93836 / GSE133502

Skinner MK, Nilsson E, Sadler-Riggleman I, Beck D, Ben Maamar M, McCarrey J (2019) Transgenerational Sperm DNA Methylation Epimutation Developmental Origins Following Ancestral Vinclozolin Exposure. Epigenetics. 14:7,721-739. PMID: 31079544. GSE117995

Sadler-Riggleman I, Klukovich R, Nilsson E, Beck D, Xie Y, Yan W, Skinner MK (2019) Epigenetic Transgenerational Inheritance of Testis Pathology and Sertoli Cell Epimutations: Generational Origins of Male Infertility. Environmental Epigenetics 5(3),1-18, dvz013. PMID: 31528361. GSE118306

King SE, McBirney M, Beck D, Sadler-Riggleman I, Nilsson E, Skinner MK (2019) Sperm Epimutation Biomarkers of Obesity and Pathologies following DDT Induced Epigenetic Transgenerational Inheritance of Disease. Environmental Epigenetics 5(2):1-15, dvz008. PMID: 31186947.  GSE114032

Kubsad D, Nilsson EE, King SE, Sadler-Riggleman I, Beck D, Skinner MK (2019) Assessment of Glyphosate Induced Epigenetic Transgenerational Inheritance of Pathologies and Sperm Epimutations: Generational Toxicology. Scientific Reports 9(1):6372. PMID: 31011160. GSE118557

Ben Maamar M, Nilsson E, Sadler-Riggleman I, Beck D, McCarrey J, Skinner MK (2019) Developmental Origins of Transgenerational Sperm DNA Methylation Epimutations Following Ancestral DDT Exposure. Developmental Biology 445:280-293. PMID: 30500333.  GSE121585

Klukovich R, Nilsson E, Sadler-Riggleman I, Beck D, Xie Y, Yan W, Skinner MK (2019) Environmental Toxicant Induced Epigenetic Transgenerational Inheritance of Prostate Pathology and Stromal-Epithelial Cell Epigenome and Transcriptome Alterations: Ancestral Origins of Prostate Disease. Scientific Reports. 18;9(1):2209. PMID: 30778168. GSE118447

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

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. 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