Skinner Laboratory

Microarray Data and R Code Files

Array Data -

Nilsson EE, Stanfield J, Skinner MK. Interactions between progesterone and tumor necrosis factor-alpha in the regulation of primordial follicle assembly. Reproduction 2006 Dec;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
 
Meachem SJ, Ruwanpura SM, Ziolkowski J, Ague JM et al. Developmentally distinct in vivo effects of FSH on proliferation and apoptosis during testis maturation. J Endocrinol 2005 Sep;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

Small CL, Shima JE, Uzumcu M, Skinner MK et al. Profiling gene expression during the differentiation and development of the murine embryonic gonad. Biol Reprod 2005 Feb;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 

Kezele PR, Ague JM, Nilsson E, Skinner MK. 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

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

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

Nilsson E, Rogers N, Skinner MK. 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

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

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

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

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

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

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

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

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

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

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

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

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

Michael K. Skinner, Marina Savenkova, Bin Zhang, Andrea Gore, David Crews.  Gene Networks Involved in Epigenetic Transgenerational Inheritance of Altered Sexual Selection: Role Environmental Epigenetics in Evolutionary Biology. 2012 Submitted.  GSE33830

Eric Nilsson, Ginger Larsen, Mohan Manikkam, Carlos Guerrero-Bosagna, Marina Savenkova, Michael K. Skinner. Environmentally Induced Epigenetic Transgenerational Inheritance of Ovarian Disease.  PLoS ONE 2012 7(5):e36129. PMID:  22570695.  GSE33423

Michael K. Skinner, Mohan Manikkam, Md. M. Haque, Bin Zhang, Marina Savenkova.  Environmentally Induced Epigenetic Transgenerational Inheritance of Somatic Transcriptomes And Associated Gene Bionetworks. 2012 Genome Biology 3;13(10):R91  GSE35839

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

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

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

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

 

R-Code Files -

ChIP-Chip Analysis

MeDIP-Chip Analysis

ComputeDiff.R

Median300Bp.R

Normalize.R

readNimblegen.R

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