Frequent Loss of Heterozygosity Targeting the Inactive X Chromosome in Melanoma
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1 Long-Read Genome Sequencing for the Diagnosis Of
bioRxiv preprint doi: https://doi.org/10.1101/2020.07.02.185447; this version posted September 14, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-ND 4.0 International license. Long-read genome sequencing for the diagnosis of neurodevelopmental disorders Susan M. Hiatt1, James M.J. Lawlor1, Lori H. Handley1, Ryne C. Ramaker1, Brianne B. Rogers1,2, E. Christopher Partridge1, Lori Beth Boston1, Melissa Williams1, Christopher B. Plott1, Jerry Jenkins1, David E. Gray1, James M. Holt1, Kevin M. Bowling1, E. Martina Bebin3, Jane Grimwood1, Jeremy Schmutz1, Gregory M. Cooper1* 1HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA, 35806 2Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA, 35924 3Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, USA, 35924 *[email protected], 256-327-9490 Conflicts of Interest The authors all declare no conflicts of interest. 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.07.02.185447; this version posted September 14, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-ND 4.0 International license. Abstract Purpose Exome and genome sequencing have proven to be effective tools for the diagnosis of neurodevelopmental disorders (NDDs), but large fractions of NDDs cannot be attributed to currently detectable genetic variation. This is likely, at least in part, a result of the fact that many genetic variants are difficult or impossible to detect through typical short-read sequencing approaches. -
Building Bonds Between NHGRI and NICHD • NICHD Has Four ABMGG Boarded Clinical Geneticists • Drs
Building Bonds Between NHGRI NICHD Diana W. Bianchi, M.D. Director, NICHD November 8, 2017 A Vision for NICHD’s Future What’s In a Name? NICHD 18% Other Institutes 82% Eunice Kennedy Shriver National Institute of Child Health and Human Development History of Our Mission ". We will look to the National Institute of Child Health and Human Development for a concentrated attack on the unsolved health problems of children and of mother-infant relationships. This legislation will encourage imaginative research into the complex processes of human development from conception to old age. For the first time, we will have an institute to promote studies directed at the entire life process rather than toward specific diseases or illnesses." —John F. Kennedy, October 17, 1962 My Vision for NICHD-I • Define “our brand” (what is our focus?) • Communicate the message • Listen to the Voice of the Patient • Integrate obstetrics and pediatrics research at NICHD; take the long view (DoHaD) • Advocate for personalized medicine in pediatrics, obstetrics and rehabilitative medicine My Vision for NICHD-II • Stress the importance of data science and sharing to leverage our investments • Analyze best way to identify trainees most likely to succeed • Catalyze innovation • Emphasize the “A” (for “Advice”) in the Advisory Council • Build bridges between other NIH Institutes – especially with NHGRI Ensure Representation of NICHD Populations in Trans-NIH Initiatives • Pregnant women can be enrolled in Phase I • Adults with intellectual disabilities can be enrolled once consent issues have been clarified • Children to be enrolled in Phase II Building Bonds Melissa Parisi MD PhD Medical Genetics Branch: Prenatal Genomics and Therapy Section • New Lab at NHGRI • Focus on Prenatal Treatment of Down syndrome • Incidental Findings Following Prenatal DNA Screening Building Bonds Between NHGRI and NICHD • NICHD has four ABMGG boarded clinical geneticists • Drs. -
Mouse Ppef1 Knockout Project (CRISPR/Cas9)
https://www.alphaknockout.com Mouse Ppef1 Knockout Project (CRISPR/Cas9) Objective: To create a Ppef1 knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering. Strategy summary: The Ppef1 gene (NCBI Reference Sequence: NM_011147 ; Ensembl: ENSMUSG00000062168 ) is located on Mouse chromosome X. 16 exons are identified, with the ATG start codon in exon 1 and the TAA stop codon in exon 16 (Transcript: ENSMUST00000071204). Exon 2~4 will be selected as target site. Cas9 and gRNA will be co-injected into fertilized eggs for KO Mouse production. The pups will be genotyped by PCR followed by sequencing analysis. Note: Homozygous null female and hemizygous null male mice are viable, fertile and display no overt abnormalities. Exon 2 starts from about 2.41% of the coding region. Exon 2~4 covers 18.41% of the coding region. The size of effective KO region: ~10105 bp. The KO region does not have any other known gene. Page 1 of 8 https://www.alphaknockout.com Overview of the Targeting Strategy Wildtype allele 5' gRNA region gRNA region 3' 1 2 3 4 16 Legends Exon of mouse Ppef1 Knockout region Page 2 of 8 https://www.alphaknockout.com Overview of the Dot Plot (up) Window size: 15 bp Forward Reverse Complement Sequence 12 Note: The 2000 bp section upstream of Exon 2 is aligned with itself to determine if there are tandem repeats. No significant tandem repeat is found in the dot plot matrix. So this region is suitable for PCR screening or sequencing analysis. Overview of the Dot Plot (down) Window size: 15 bp Forward Reverse Complement Sequence 12 Note: The 2000 bp section downstream of Exon 4 is aligned with itself to determine if there are tandem repeats. -
SMARCA1 Antibody A
Revision 1 C 0 2 - t SMARCA1 Antibody a e r o t S Orders: 877-616-CELL (2355) [email protected] Support: 877-678-TECH (8324) 0 5 Web: [email protected] 4 www.cellsignal.com 9 # 3 Trask Lane Danvers Massachusetts 01923 USA For Research Use Only. Not For Use In Diagnostic Procedures. Applications: Reactivity: Sensitivity: MW (kDa): Source: UniProt ID: Entrez-Gene Id: WB, IP H Endogenous 130 Rabbit P28370 6594 Product Usage Information 5. Ho, L. and Crabtree, G.R. (2010) Nature 463, 474-84. 6. Landry, J.W. et al. (2011) Genes Dev 25, 275-86. Application Dilution 7. Landry, J. et al. (2008) PLoS Genet 4, e1000241. Western Blotting 1:1000 Immunoprecipitation 1:50 Storage Supplied in 10 mM sodium HEPES (pH 7.5), 150 mM NaCl, 100 µg/ml BSA and 50% glycerol. Store at –20°C. Do not aliquot the antibody. Specificity / Sensitivity SMARCA1 Antibody recognizes endogenous levels of total SMARCA1 protein. Species Reactivity: Human Source / Purification Polyclonal antibodies are produced by immunizing animals with a synthetic peptide corresponding to residues near the amino terminus of human SMARCA1 protein. Antibodies are purified by protein A and peptide affinity chromatography. Background SMARCA1 (SNF2L) is one of the two orthologs of the ISWI (imitation switch) ATPases encoded by the mammalian genome (1). The ISWI chromatin remodeling complexes were first identified in Drosophila and have been shown to remodel and alter nucleosome spacing in vitro (2). SMARCA1 is the catalytic subunit of the nucleosome remodeling factor (NURF) and CECR2-containing remodeling factor (CERF) complexes (3-5). -
Identification of Conserved Genes Triggering Puberty in European Sea
Blázquez et al. BMC Genomics (2017) 18:441 DOI 10.1186/s12864-017-3823-2 RESEARCHARTICLE Open Access Identification of conserved genes triggering puberty in European sea bass males (Dicentrarchus labrax) by microarray expression profiling Mercedes Blázquez1,2* , Paula Medina1,2,3, Berta Crespo1,4, Ana Gómez1 and Silvia Zanuy1* Abstract Background: Spermatogenesisisacomplexprocesscharacterized by the activation and/or repression of a number of genes in a spatio-temporal manner. Pubertal development in males starts with the onset of the first spermatogenesis and implies the division of primary spermatogonia and their subsequent entry into meiosis. This study is aimed at the characterization of genes involved in the onset of puberty in European sea bass, and constitutes the first transcriptomic approach focused on meiosis in this species. Results: European sea bass testes collected at the onset of puberty (first successful reproduction) were grouped in stage I (resting stage), and stage II (proliferative stage). Transition from stage I to stage II was marked by an increase of 11ketotestosterone (11KT), the main fish androgen, whereas the transcriptomic study resulted in 315 genes differentially expressed between the two stages. The onset of puberty induced 1) an up-regulation of genes involved in cell proliferation, cell cycle and meiosis progression, 2) changes in genes related with reproduction and growth, and 3) a down-regulation of genes included in the retinoic acid (RA) signalling pathway. The analysis of GO-terms and biological pathways showed that cell cycle, cell division, cellular metabolic processes, and reproduction were affected, consistent with the early events that occur during the onset of puberty. -
Monoclonal Antibody to SMARCA1
AM50455PU-N OriGene Technologies Inc. OriGene EU Acris Antibodies GmbH 9620 Medical Center Drive, Ste 200 Schillerstr. 5 Rockville, MD 20850 32052 Herford UNITED STATES GERMANY Phone: +1-888-267-4436 Phone: +49-5221-34606-0 Fax: +1-301-340-8606 Fax: +49-5221-34606-11 [email protected] [email protected] Monoclonal Antibody to SMARCA1 - Purified Alternate names: ATP-dependent helicase SMARCA1, Nucleosome-remodeling factor subunit SNF2L, Probable global transcription activator SNF2L1, SNF2L, SNF2L1, SWI/SNF-related matrix- associated actin-dependent regulator of chromatin subfamily A member 1 Catalog No.: AM50455PU-N Quantity: 0.1 mg Concentration: lot-specific Background: Nucleosome-remodeling factor subunit SNF2L, also known as SWI/SNF-related matrix- associated actin-dependent regulator of chromatin subfamily A member 1 (SMARCA1), is the energy-transducing component of NURF (nucleosome-remodeling factor) and CERF (CECR2-containing-remodeling factor) complexes. These complexes facilitate the disruption of chromatin structure in an ATP-dependent manner. SNF2L potentiates neurite outgrowth, and may be involved in brain development by regulating En-1 and En-2 expression as well as in the development of luteal cells. Uniprot ID: P28370 NCBI: NP_003060.2 GeneID: 6594 Host / Isotype: Rat / IgG2b Clone: SNF 2C4 Immunogen: GST-tagged recombinant protein corresponding to human SNF2L. Format: State: Liquid purified Ig fraction Purification: Protein G Chromatography Buffer System: 0.1 M Tris-Glycine (pH 7.4), 150 mM NaCl with 0.05% sodium azide. Applications: Immunohistochemistry: A representative lot was used by an an independent laboratory to detect SNF2L in certain, normal human organ tissues. (Eckey, M., et al. -
SMARCA1 (D4Q7V) Rabbit
SMARCA1 (D4Q7V) Rabbit mAb Store at -20°C 3 n 100 µl Orders n 877-616-CELL (2355) (10 western blots) [email protected] Support n 877-678-TECH (8324) [email protected] Web n www.cellsignal.com New 03/13 #12483 For Research Use Only. Not For Use In Diagnostic Procedures. Entrez-Gene ID #6594 Swiss-Prot Acc. #P28370 Storage: Supplied in 10 mM sodium HEPES (pH 7.5), 150 Applications Species Cross-Reactivity* Molecular Wt. Isotype mM NaCl, 100 µg/ml BSA, 50% glycerol and less than 0.02% W, IP H, Mk 130 kDa Rabbit IgG** sodium azide. Store at –20°C. Do not aliquot the antibody. Endogenous *Species cross-reactivity is determined by western blot. Background: SMARCA1 (SNF2L) is one of the two ortho- ** Anti-rabbit secondary antibodies must be used to logs of the ISWI (imitation switch) ATPases encoded by the detect this antibody. kDa LN18 SW620 HeLa HT-29 Saos-2 OVCAR8COS-7 mammalian genome (1). The ISWI chromatin remodeling Recommended Antibody Dilutions: complexes were first identified in Drosophila and have been 200 140 Western blotting 1:1000 shown to remodel and alter nucleosome spacing in vitro (2). SMARCA1 100 Immunoprecipitation 1:100 SMARCA1 is the catalytic subunit of the nucleosome re- 80 modeling factor (NURF) and CECR2-containing remodeling For product specific protocols please see the web page 60 factor (CERF) complexes (3-5). The NURF complex plays an 50 for this product at www.cellsignal.com. important role in neuronal physiology by promoting neurite 40 Please visit www.cellsignal.com for a complete listing outgrowth and regulation of Engrailed homeotic genes that 30 of recommended complementary products. -
Contribution of Multiple Inherited Variants to Autism Spectrum Disorder (ASD) in a Family with 3 Affected Siblings
G C A T T A C G G C A T genes Article Contribution of Multiple Inherited Variants to Autism Spectrum Disorder (ASD) in a Family with 3 Affected Siblings Jasleen Dhaliwal 1 , Ying Qiao 1,2, Kristina Calli 1,2, Sally Martell 1,2, Simone Race 3,4,5, Chieko Chijiwa 1,5, Armansa Glodjo 3,5, Steven Jones 1,6 , Evica Rajcan-Separovic 2,7, Stephen W. Scherer 4 and Suzanne Lewis 1,2,5,* 1 Department of Medical Genetics, University of British Columbia (UBC), Vancouver, BC V6H 3N1, Canada; [email protected] (J.D.); [email protected] (Y.Q.); [email protected] (K.C.); [email protected] (S.M.); [email protected] (C.C.); [email protected] (S.J.) 2 BC Children’s Hospital, Vancouver, BC V5Z 4H4, Canada; [email protected] 3 Department of Pediatrics, University of British Columbia (UBC), Vancouver, BC V6T 1Z7, Canada; [email protected] (S.R.); [email protected] (A.G.) 4 The Centre for Applied Genomics and McLaughlin Centre, Hospital for Sick Children and University of Toronto, Toronto, ON M5G 0A4, Canada; [email protected] 5 BC Children’s and Women’s Health Center, Vancouver, BC V6H 3N1, Canada 6 Michael Smith Genome Sciences Centre, Vancouver, BC V5Z 4S6, Canada 7 Department of Pathology and Laboratory Medicine, University of British Columbia (UBC), Vancouver, BC V6T 1Z7, Canada * Correspondence: [email protected] Abstract: Autism Spectrum Disorder (ASD) is the most common neurodevelopmental disorder in Citation: Dhaliwal, J.; Qiao, Y.; Calli, children and shows high heritability. -
Small Cell Carcinoma of the Ovary, Hypercalcemic Type (SCCOHT) Beyond SMARCA4 Mutations: a Comprehensive Genomic Analysis
cells Article Small Cell Carcinoma of the Ovary, Hypercalcemic Type (SCCOHT) beyond SMARCA4 Mutations: A Comprehensive Genomic Analysis Aurélie Auguste 1,Félix Blanc-Durand 2 , Marc Deloger 3 , Audrey Le Formal 1, Rohan Bareja 4,5, David C. Wilkes 4 , Catherine Richon 6,Béatrice Brunn 2, Olivier Caron 6, Mojgan Devouassoux-Shisheboran 7,Sébastien Gouy 2, Philippe Morice 2, Enrica Bentivegna 2, Andrea Sboner 4,5,8, Olivier Elemento 4,8, Mark A. Rubin 9 , Patricia Pautier 2, Catherine Genestie 10, Joanna Cyrta 4,9,11 and Alexandra Leary 1,2,* 1 Medical Oncologist, Gynecology Unit, Lead Translational Research Team, INSERM U981, Gustave Roussy, 94805 Villejuif, France; [email protected] (A.A.); [email protected] (A.L.F.) 2 Gynecological Unit, Department of Medicine, Gustave Roussy, 94805 Villejuif, France; [email protected] (F.B.-D.); [email protected] (B.B.); [email protected] (S.G.); [email protected] (P.M.); [email protected] (E.B.); [email protected] (P.P.) 3 Bioinformatics Core Facility, Gustave Roussy Cancer Center, UMS CNRS 3655/INSERM 23 AMMICA, 94805 Villejuif, France; [email protected] 4 Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10001, USA; [email protected] (R.B.); [email protected] (D.C.W.); [email protected] (A.S.); [email protected] (O.E.); [email protected] (J.C.) 5 Institute for Computational Biomedicine, Weill Cornell -
PPEF1 Monoclonal Antibody (M01), Clone 1F6-1A5
PPEF1 monoclonal antibody (M01), clone 1F6-1A5 Catalog # : H00005475-M01 規格 : [ 100 ug ] List All Specification Application Image Product Mouse monoclonal antibody raised against a full length recombinant Western Blot (Transfected lysate) Description: PPEF1. Immunogen: PPEF1 (AAH36026, 1 a.a. ~ 653 a.a) full-length recombinant protein with GST tag. MW of the GST tag alone is 26 KDa. Sequence: MGCSSSSTKTRRSDTSLRAALIIQNWYRGYKARLKARQHYALTIFQSIEY ADEQGQMQLSTFFSFMLENYTHIHKEELELRNQSLESEQDMRDRWDYV DSIDVPDSYNGPRLQFPLTCTDIDLLLEAFKEQQILHAHYVLEVLFETKKV enlarge LKQMPNFTHIQTSPSKEVTICGDLHGKLDDLFLIFYKNGLPSERNPYVFNG Western Blot (Recombinant DFVDRGKNSIEILMILCVSFLVYPNDLHLNRGNHEDFMMNLRYGFTKEILH protein) KYKLHGKRILQILEEFYAWLPIGTIVDNEILVIHGGISETTDLNLLHRVERNK MKSVLIPPTETNRDHDTDSKHNKVGVTFNAHGRIKTNGSPTEHLTEHEWE ELISA QIIDILWSDPRGKNGCFPNTCRGGGCYFGPDVTSKILNKYQLKMLIRSHE CKPEGYEICHDGKVVTIFSASNYYEEGSNRGAYIKLCSGTTPRFFQYQVT RNAi Knockdown (Antibody KATCFQPLRQRVDTMENSAIKILRERVISRKSDLTRAFQLQDHRKSGKLS validated) VSQWAFCMENILGLNLPWRSLSSNLVNIDQNGNVEYMSSFQNIRIEKPVQ EAHSTLVETLYRYRSDLEIIFNAIDTDHSGLISVEEFRAMWKLFSSHYNVHI DDSQVNKLANIMDLNKDGSIDFNEFLKAFYVVHRYEDLMKPDVTNLG Host: Mouse Reactivity: Human enlarge Isotype: IgG1 Kappa Quality Control Antibody Reactive Against Recombinant Protein. Testing: Western Blot detection against Immunogen (97.57 KDa) . Storage Buffer: In 1x PBS, pH 7.4 Storage Store at -20°C or lower. Aliquot to avoid repeated freezing and thawing. Instruction: MSDS: Download Datasheet: Download Applications Page 1 of 3 2016/5/21 Western Blot (Transfected lysate) -
The H3K9 Methylation Writer SETDB1 and Its Reader MPP8 Cooperate to Silence Satellite DNA Repeats in Mouse Embryonic Stem Cells
G C A T T A C G G C A T genes Article The H3K9 Methylation Writer SETDB1 and Its Reader MPP8 Cooperate to Silence Satellite DNA Repeats in Mouse Embryonic Stem Cells 1,2,3,4 1 1, 1 Paola Cruz-Tapias , Philippe Robin , Julien Pontis y, Laurence Del Maestro and Slimane Ait-Si-Ali 1,* 1 Epigenetics and Cell Fate (EDC), Centre National de la Recherche Scientifique (CNRS), Université de Paris, Université Paris Diderot, F-75013 Paris, France; [email protected] (P.C.-T.); [email protected] (P.R.); julien.pontis@epfl.ch (J.P.); [email protected] (L.D.M.) 2 Faculty of Natural Sciences and Mathematics, Universidad del Rosario, Bogotá 111221, Colombia 3 School of Medicine and Health Sciences, Universidad del Rosario, Bogotá 111221, Colombia 4 Doctoral Program in Biomedical and Biological Sciences, Universidad del Rosario, Bogotá 111221, Colombia * Correspondence: [email protected]; Tel.: +33-(0)1-5727-8919 Current: Ecole Polytechnique Fédérale de Lausanne (EPFL), SV LVG Station 19, 1015 Lausanne, Switzerland. y Received: 25 August 2019; Accepted: 24 September 2019; Published: 25 September 2019 Abstract: SETDB1 (SET Domain Bifurcated histone lysine methyltransferase 1) is a key lysine methyltransferase (KMT) required in embryonic stem cells (ESCs), where it silences transposable elements and DNA repeats via histone H3 lysine 9 tri-methylation (H3K9me3), independently of DNA methylation. The H3K9 methylation reader M-Phase Phosphoprotein 8 (MPP8) is highly expressed in ESCs and germline cells. Although evidence of a cooperation between H3K9 KMTs and MPP8 in committed cells has emerged, the interplay between H3K9 methylation writers and MPP8 in ESCs remains elusive. -
Comparative Transcriptome Profiling of the Human and Mouse Dorsal Root Ganglia: an RNA-Seq-Based Resource for Pain and Sensory Neuroscience Research
bioRxiv preprint doi: https://doi.org/10.1101/165431; this version posted October 13, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Title: Comparative transcriptome profiling of the human and mouse dorsal root ganglia: An RNA-seq-based resource for pain and sensory neuroscience research Short Title: Human and mouse DRG comparative transcriptomics Pradipta Ray 1, 2 #, Andrew Torck 1 , Lilyana Quigley 1, Andi Wangzhou 1, Matthew Neiman 1, Chandranshu Rao 1, Tiffany Lam 1, Ji-Young Kim 1, Tae Hoon Kim 2, Michael Q. Zhang 2, Gregory Dussor 1 and Theodore J. Price 1, # 1 The University of Texas at Dallas, School of Behavioral and Brain Sciences 2 The University of Texas at Dallas, Department of Biological Sciences # Corresponding authors Theodore J Price Pradipta Ray School of Behavioral and Brain Sciences School of Behavioral and Brain Sciences The University of Texas at Dallas The University of Texas at Dallas BSB 14.102G BSB 10.608 800 W Campbell Rd 800 W Campbell Rd Richardson TX 75080 Richardson TX 75080 972-883-4311 972-883-7262 [email protected] [email protected] Number of pages: 27 Number of figures: 9 Number of tables: 8 Supplementary Figures: 4 Supplementary Files: 6 Word count: Abstract = 219; Introduction = 457; Discussion = 1094 Conflict of interest: The authors declare no conflicts of interest Patient anonymity and informed consent: Informed consent for human tissue sources were obtained by Anabios, Inc. (San Diego, CA). Human studies: This work was approved by The University of Texas at Dallas Institutional Review Board (MR 15-237).