Anti-SNAPC1 (Internal Region) Polyclonal Antibody (DPABH-27248) This Product Is for Research Use Only and Is Not Intended for Diagnostic Use

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Anti-SNAPC1 (internal region) polyclonal antibody (DPABH-27248) This product is for research use only and is not intended for diagnostic use. PRODUCT INFORMATION Antigen Description Part of the SNAPc complex required for the transcription of both RNA polymerase II and III small- nuclear RNA genes. Binds to the proximal sequence element (PSE), a non-TATA-box basal promoter element common to these 2 types of genes. Recruits TBP and BRF2 to the U6 snRNA TATA box. Immunogen Synthetic peptide, derived from an internal region of Mouse SNAP43 (UniProt ID: Q8K0S9). Isotype IgG Source/Host Rabbit Species Reactivity Mouse Purification Whole antiserum Conjugate Unconjugated Applications WB, ICC Format Liquid Size 200 μl Buffer Constituent: Whole serum Preservative None Storage Store at 4°C short term (1-2 weeks). Aliquot and store at -20°C long term. Avoid repeated freeze / thaw cycles. GENE INFORMATION Gene Name SNAPC1 small nuclear RNA activating complex, polypeptide 2 [ Mus musculus ] Official Symbol SNAPC1 Synonyms SNAPC1; small nuclear RNA activating complex, polypeptide 1; AU015787; 2700033G17Rik; snRNA-activating protein complex subunit 1; SNAPc subunit 1; SNAPc 43 kDa subunit; snRNA- 45-1 Ramsey Road, Shirley, NY 11967, USA Email: [email protected] Tel: 1-631-624-4882 Fax: 1-631-938-8221 1 © Creative Diagnostics All Rights Reserved activating protein complex 43 kDa subunit; small nuclear RNA-activating complex polypeptide 1; Entrez Gene ID 75627 Protein Refseq NP_848479.1 UniProt ID Q8K0S9 Pathway Gene Expression; RNA Polymerase III Abortive And Retractive Initiation; RNA Polymerase III Transcription Initiation; Function DNA binding; molecular_function; 45-1 Ramsey Road, Shirley, NY 11967, USA Email: [email protected] Tel: 1-631-624-4882 Fax: 1-631-938-8221 2 © Creative Diagnostics All Rights Reserved.

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PARSANA-DISSERTATION-2020.Pdf
DECIPHERING TRANSCRIPTIONAL PATTERNS OF GENE REGULATION: A COMPUTATIONAL APPROACH by Princy Parsana A dissertation submitted to The Johns Hopkins University in conformity with the requirements for the degree of Doctor of Philosophy Baltimore, Maryland July, 2020 © 2020 Princy Parsana All rights reserved Abstract With rapid advancements in sequencing technology, we now have the ability to sequence the entire human genome, and to quantify expression of tens of thousands of genes from hundreds of individuals. This provides an extraordinary opportunity to learn phenotype relevant genomic patterns that can improve our understanding of molecular and cellular processes underlying a trait. The high dimensional nature of genomic data presents a range of computational and statistical challenges. This dissertation presents a compilation of projects that were driven by the motivation to efficiently capture gene regulatory patterns in the human transcriptome, while addressing statistical and computational challenges that accompany this data. We attempt to address two major difficulties in this domain: a) artifacts and noise in transcriptomic data, andb) limited statistical power. First, we present our work on investigating the effect of artifactual variation in gene expression data and its impact on trans-eQTL discovery. Here we performed an in-depth analysis of diverse pre-recorded covariates and latent confounders to understand their contribution to heterogeneity in gene expression measurements. Next, we discovered 673 trans-eQTLs across 16 human tissues using v6 data from the Genotype Tissue Expression (GTEx) project. Finally, we characterized two trait-associated trans-eQTLs; one in Skeletal Muscle and another in Thyroid. Second, we present a principal component based residualization method to correct gene expression measurements prior to reconstruction of co-expression networks.
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Distinguishing Pleiotropy from Linked QTL Between Milk Production Traits
Cai et al. Genet Sel Evol (2020) 52:19 https://doi.org/10.1186/s12711-020-00538-6 Genetics Selection Evolution RESEARCH ARTICLE Open Access Distinguishing pleiotropy from linked QTL between milk production traits and mastitis resistance in Nordic Holstein cattle Zexi Cai1*†, Magdalena Dusza2†, Bernt Guldbrandtsen1, Mogens Sandø Lund1 and Goutam Sahana1 Abstract Background: Production and health traits are central in cattle breeding. Advances in next-generation sequencing technologies and genotype imputation have increased the resolution of gene mapping based on genome-wide association studies (GWAS). Thus, numerous candidate genes that afect milk yield, milk composition, and mastitis resistance in dairy cattle are reported in the literature. Efect-bearing variants often afect multiple traits. Because the detection of overlapping quantitative trait loci (QTL) regions from single-trait GWAS is too inaccurate and subjective, multi-trait analysis is a better approach to detect pleiotropic efects of variants in candidate genes. However, large sample sizes are required to achieve sufcient power. Multi-trait meta-analysis is one approach to deal with this prob- lem. Thus, we performed two multi-trait meta-analyses, one for three milk production traits (milk yield, protein yield and fat yield), and one for milk yield and mastitis resistance. Results: For highly correlated traits, the power to detect pleiotropy was increased by multi-trait meta-analysis com- pared with the subjective assessment of overlapping of single-trait QTL confdence intervals. Pleiotropic efects of lead single nucleotide polymorphisms (SNPs) that were detected from the multi-trait meta-analysis were confrmed by bivariate association analysis. The previously reported pleiotropic efects of variants within the DGAT1 and MGST1 genes on three milk production traits, and pleiotropic efects of variants in GHR on milk yield and fat yield were con- frmed.
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Noelia Díaz Blanco
Effects of environmental factors on the gonadal transcriptome of European sea bass (Dicentrarchus labrax), juvenile growth and sex ratios Noelia Díaz Blanco Ph.D. thesis 2014 Submitted in partial fulfillment of the requirements for the Ph.D. degree from the Universitat Pompeu Fabra (UPF). This work has been carried out at the Group of Biology of Reproduction (GBR), at the Department of Renewable Marine Resources of the Institute of Marine Sciences (ICM-CSIC). Thesis supervisor: Dr. Francesc Piferrer Professor d’Investigació Institut de Ciències del Mar (ICM-CSIC) i ii A mis padres A Xavi iii iv Acknowledgements This thesis has been made possible by the support of many people who in one way or another, many times unknowingly, gave me the strength to overcome this "long and winding road". First of all, I would like to thank my supervisor, Dr. Francesc Piferrer, for his patience, guidance and wise advice throughout all this Ph.D. experience. But above all, for the trust he placed on me almost seven years ago when he offered me the opportunity to be part of his team. Thanks also for teaching me how to question always everything, for sharing with me your enthusiasm for science and for giving me the opportunity of learning from you by participating in many projects, collaborations and scientific meetings. I am also thankful to my colleagues (former and present Group of Biology of Reproduction members) for your support and encouragement throughout this journey. To the “exGBRs”, thanks for helping me with my first steps into this world. Working as an undergrad with you Dr.
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Genomic Study of RNA Polymerase II and III Snapc-Bound Promoters Reveals a Gene Transcribed by Both Enzymes and a Broad Use of Common Activators
Genomic Study of RNA Polymerase II and III SNAPc-Bound Promoters Reveals a Gene Transcribed by Both Enzymes and a Broad Use of Common Activators Nicole James Faresse1., Donatella Canella1., Viviane Praz1,2, Joe¨lle Michaud1¤, David Romascano1, Nouria Hernandez1* 1 Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland, 2 Swiss Institute of Bioinformatics, Lausanne, Switzerland Abstract SNAPc is one of a few basal transcription factors used by both RNA polymerase (pol) II and pol III. To define the set of active SNAPc-dependent promoters in human cells, we have localized genome-wide four SNAPc subunits, GTF2B (TFIIB), BRF2, pol II, and pol III. Among some seventy loci occupied by SNAPc and other factors, including pol II snRNA genes, pol III genes with type 3 promoters, and a few un-annotated loci, most are primarily occupied by either pol II and GTF2B, or pol III and BRF2. A notable exception is the RPPH1 gene, which is occupied by significant amounts of both polymerases. We show that the large majority of SNAPc-dependent promoters recruit POU2F1 and/or ZNF143 on their enhancer region, and a subset also recruits GABP, a factor newly implicated in SNAPc-dependent transcription. These activators associate with pol II and III promoters in G1 slightly before the polymerase, and ZNF143 is required for efficient transcription initiation complex assembly. The results characterize a set of genes with unique properties and establish that polymerase specificity is not absolute in vivo. Citation: James Faresse N, Canella D, Praz V, Michaud J, Romascano D, et al.
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Mapping of a Chromosome 12 Region Associated with Airway Hyperresponsiveness in a Recombinant Congenic Mouse Strain and Selection of Potential Candidate Genes by Expression and Sequence Variation Analyses Cynthia Kanagaratham1*, Rafael Marino2, Pierre Camateros2, John Ren3, Daniel Houle4, Robert Sladek1,2,5, Silvia M. Vidal1,3, Danuta Radzioch1,2 1 Department of Human Genetics, McGill University, Montreal, Quebec, Canada, 2 Faculty of Medicine, Division of Experimental Medicine, McGill University, Montreal, Quebec, Canada, 3 Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada, 4 Research Institute of the McGill University Health Center, Montreal, Quebec, Canada, 5 McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada Abstract In a previous study we determined that BcA86 mice, a strain belonging to a panel of AcB/BcA recombinant congenic strains, have an airway responsiveness phenotype resembling mice from the airway hyperresponsive A/J strain. The majority of the BcA86 genome is however from the hyporesponsive C57BL/6J strain. The aim of this study was to identify candidate regions and genes associated with airway hyperresponsiveness (AHR) by quantitative trait locus (QTL) analysis using the BcA86 strain. Airway responsiveness of 205 F2 mice generated from backcrossing BcA86 strain to C57BL/6J strain was measured and used for QTL analysis to identify genomic regions in linkage with AHR. Consomic mice for the QTL containing chromosomes were phenotyped to study the contribution of each chromosome to lung responsiveness. Candidate genes within the QTL were selected based on expression differences in mRNA from whole lungs, and the presence of coding non- synonymous mutations that were predicted to have a functional effect by amino acid substitution prediction tools.
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bioRxiv preprint doi: https://doi.org/10.1101/2020.06.29.177642; this version posted June 29, 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-NC-ND 4.0 International license. Cryo-EM structures of human RNA polymerase III in its unbound and transcribing states Mathias Girbig1,3,4, Agata D. Misiaszek1,3,4, Matthias K. Vorländer1, Aleix Lafita2, Helga Grötsch1, Florence Baudin1, Alex Bateman2, Christoph W. Müller1* 1European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany. 2European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK. 3Candidate for joint PhD degree from EMBL and Heidelberg University, Faculty of Biosciences, 69120 Heidelberg, Germany. 4These authors contributed equally: Mathias Girbig, Agata D. Misiaszek. * Correspondence to CWM ([email protected]) 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.06.29.177642; this version posted June 29, 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-NC-ND 4.0 International license. ABSTRACT RNA polymerase III (Pol III) synthesises tRNAs and other short, essential RNAs. Human Pol III misregulation is linked to tumour transformation, neurodegenerative and developmental disorders, and increased sensitivity to viral infections. Pol III inhibition increases longevity in different animals but also promotes intracellular bacterial growth owing to its role in the immune system.
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Rabbit Anti-SNAPC3/FITC Conjugated Antibody
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