GSGS: a Computational Framework to Reconstruct Signaling Pathways
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POLR2I Antibody (Monoclonal) (M01) Mouse Monoclonal Antibody Raised Against a Partial Recombinant POLR2I
10320 Camino Santa Fe, Suite G San Diego, CA 92121 Tel: 858.875.1900 Fax: 858.622.0609 POLR2I Antibody (monoclonal) (M01) Mouse monoclonal antibody raised against a partial recombinant POLR2I. Catalog # AT3377a Specification POLR2I Antibody (monoclonal) (M01) - Product Information Application WB, E Primary Accession P36954 Other Accession BC017112 Reactivity Human Host mouse Clonality Monoclonal Isotype IgG1 Kappa Calculated MW 14523 POLR2I Antibody (monoclonal) (M01) - Additional Information Antibody Reactive Against Recombinant Protein.Western Blot detection against Gene ID 5438 Immunogen (36.74 KDa) . Other Names DNA-directed RNA polymerase II subunit RPB9, RNA polymerase II subunit B9, DNA-directed RNA polymerase II subunit I, RNA polymerase II 145 kDa subunit, RPB145, POLR2I Target/Specificity POLR2I (AAH17112, 26 a.a. ~ 125 a.a) partial recombinant protein with GST tag. MW of the GST tag alone is 26 KDa. Detection limit for recombinant GST tagged Dilution POLR2I is approximately 0.03ng/ml as a WB~~1:500~1000 capture antibody. Format Clear, colorless solution in phosphate POLR2I Antibody (monoclonal) (M01) - buffered saline, pH 7.2 . Background Storage This gene encodes a subunit of RNA Store at -20°C or lower. Aliquot to avoid polymerase II, the polymerase responsible for repeated freezing and thawing. synthesizing messenger RNA in eukaryotes. This subunit, in combination with two other Precautions polymerase subunits, forms the DNA binding POLR2I Antibody (monoclonal) (M01) is for domain of the polymerase, a groove in which research use only and not for use in the DNA template is transcribed into RNA. The diagnostic or therapeutic procedures. product of this gene has two zinc finger motifs with conserved cysteines and the subunit does possess zinc binding activity. -
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Spectrum Name of Protein Count of Peptides Ratio (POL2RA/IgG control) POLR2A_228kdBand POLR2A DNA-directed RNA polymerase II subunit RPB1 197 NOT IN CONTROL IP POLR2A_228kdBand POLR2B DNA-directed RNA polymerase II subunit RPB2 146 NOT IN CONTROL IP POLR2A_228kdBand RPAP2 Isoform 1 of RNA polymerase II-associated protein 2 24 NOT IN CONTROL IP POLR2A_228kdBand POLR2G DNA-directed RNA polymerase II subunit RPB7 23 NOT IN CONTROL IP POLR2A_228kdBand POLR2H DNA-directed RNA polymerases I, II, and III subunit RPABC3 19 NOT IN CONTROL IP POLR2A_228kdBand POLR2C DNA-directed RNA polymerase II subunit RPB3 17 NOT IN CONTROL IP POLR2A_228kdBand POLR2J RPB11a protein 7 NOT IN CONTROL IP POLR2A_228kdBand POLR2E DNA-directed RNA polymerases I, II, and III subunit RPABC1 8 NOT IN CONTROL IP POLR2A_228kdBand POLR2I DNA-directed RNA polymerase II subunit RPB9 9 NOT IN CONTROL IP POLR2A_228kdBand ALMS1 ALMS1 3 NOT IN CONTROL IP POLR2A_228kdBand POLR2D DNA-directed RNA polymerase II subunit RPB4 6 NOT IN CONTROL IP POLR2A_228kdBand GRINL1A;Gcom1 Isoform 12 of Protein GRINL1A 6 NOT IN CONTROL IP POLR2A_228kdBand RECQL5 Isoform Beta of ATP-dependent DNA helicase Q5 3 NOT IN CONTROL IP POLR2A_228kdBand POLR2L DNA-directed RNA polymerases I, II, and III subunit RPABC5 5 NOT IN CONTROL IP POLR2A_228kdBand KRT6A Keratin, type II cytoskeletal 6A 3 NOT IN CONTROL IP POLR2A_228kdBand POLR2K DNA-directed RNA polymerases I, II, and III subunit RPABC4 2 NOT IN CONTROL IP POLR2A_228kdBand RFC4 Replication factor C subunit 4 1 NOT IN CONTROL IP POLR2A_228kdBand RFC2 -
A High Resolution Physical and RH Map of Pig Chromosome 6Q1.2 And
A high resolution physical and RH map of pig chromosome 6q1.2 and comparative analysis with human chromosome 19q13.1 Flávia Martins-Wess, Denis Milan, Cord Drögemüller, Rodja Voβ-Nemitz, Bertram Brenig, Annie Robic, Martine Yerle, Tosso Leeb To cite this version: Flávia Martins-Wess, Denis Milan, Cord Drögemüller, Rodja Voβ-Nemitz, Bertram Brenig, et al.. A high resolution physical and RH map of pig chromosome 6q1.2 and comparative analysis with human chromosome 19q13.1. BMC Genomics, BioMed Central, 2003, 4, pp.435-444. 10.1186/1471-2164-4- 20. hal-02680244 HAL Id: hal-02680244 https://hal.inrae.fr/hal-02680244 Submitted on 31 May 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. BMC Genomics BioMed Central Research article Open Access A high resolution physical and RH map of pig chromosome 6q1.2 and comparative analysis with human chromosome 19q13.1 Flávia Martins-Wess1, Denis Milan*2, Cord Drögemüller1, Rodja Voβ- Nemitz1, Bertram Brenig3, Annie Robic2, Martine Yerle2 and Tosso Leeb*1 Address: 1Institute of Animal Breeding and Genetics, School of Veterinary Medicine Hannover, Bünteweg 17p, 30559 Hannover, Germany, 2Institut National de la Recherche Agronomique (INRA), Laboratoire de Génétique Cellulaire, BP27, 31326 Castanet Tolosan Cedex, France and 3Institute of Veterinary Medicine, University of Göttingen, Groner Landstr. -
The Human Genome Project
TO KNOW OURSELVES ❖ THE U.S. DEPARTMENT OF ENERGY AND THE HUMAN GENOME PROJECT JULY 1996 TO KNOW OURSELVES ❖ THE U.S. DEPARTMENT OF ENERGY AND THE HUMAN GENOME PROJECT JULY 1996 Contents FOREWORD . 2 THE GENOME PROJECT—WHY THE DOE? . 4 A bold but logical step INTRODUCING THE HUMAN GENOME . 6 The recipe for life Some definitions . 6 A plan of action . 8 EXPLORING THE GENOMIC LANDSCAPE . 10 Mapping the terrain Two giant steps: Chromosomes 16 and 19 . 12 Getting down to details: Sequencing the genome . 16 Shotguns and transposons . 20 How good is good enough? . 26 Sidebar: Tools of the Trade . 17 Sidebar: The Mighty Mouse . 24 BEYOND BIOLOGY . 27 Instrumentation and informatics Smaller is better—And other developments . 27 Dealing with the data . 30 ETHICAL, LEGAL, AND SOCIAL IMPLICATIONS . 32 An essential dimension of genome research Foreword T THE END OF THE ROAD in Little has been rapid, and it is now generally agreed Cottonwood Canyon, near Salt that this international project will produce Lake City, Alta is a place of the complete sequence of the human genome near-mythic renown among by the year 2005. A skiers. In time it may well And what is more important, the value assume similar status among molecular of the project also appears beyond doubt. geneticists. In December 1984, a conference Genome research is revolutionizing biology there, co-sponsored by the U.S. Department and biotechnology, and providing a vital of Energy, pondered a single question: Does thrust to the increasingly broad scope of the modern DNA research offer a way of detect- biological sciences. -
Nº Ref Uniprot Proteína Péptidos Identificados Por MS/MS 1 P01024
Document downloaded from http://www.elsevier.es, day 26/09/2021. This copy is for personal use. Any transmission of this document by any media or format is strictly prohibited. Nº Ref Uniprot Proteína Péptidos identificados 1 P01024 CO3_HUMAN Complement C3 OS=Homo sapiens GN=C3 PE=1 SV=2 por 162MS/MS 2 P02751 FINC_HUMAN Fibronectin OS=Homo sapiens GN=FN1 PE=1 SV=4 131 3 P01023 A2MG_HUMAN Alpha-2-macroglobulin OS=Homo sapiens GN=A2M PE=1 SV=3 128 4 P0C0L4 CO4A_HUMAN Complement C4-A OS=Homo sapiens GN=C4A PE=1 SV=1 95 5 P04275 VWF_HUMAN von Willebrand factor OS=Homo sapiens GN=VWF PE=1 SV=4 81 6 P02675 FIBB_HUMAN Fibrinogen beta chain OS=Homo sapiens GN=FGB PE=1 SV=2 78 7 P01031 CO5_HUMAN Complement C5 OS=Homo sapiens GN=C5 PE=1 SV=4 66 8 P02768 ALBU_HUMAN Serum albumin OS=Homo sapiens GN=ALB PE=1 SV=2 66 9 P00450 CERU_HUMAN Ceruloplasmin OS=Homo sapiens GN=CP PE=1 SV=1 64 10 P02671 FIBA_HUMAN Fibrinogen alpha chain OS=Homo sapiens GN=FGA PE=1 SV=2 58 11 P08603 CFAH_HUMAN Complement factor H OS=Homo sapiens GN=CFH PE=1 SV=4 56 12 P02787 TRFE_HUMAN Serotransferrin OS=Homo sapiens GN=TF PE=1 SV=3 54 13 P00747 PLMN_HUMAN Plasminogen OS=Homo sapiens GN=PLG PE=1 SV=2 48 14 P02679 FIBG_HUMAN Fibrinogen gamma chain OS=Homo sapiens GN=FGG PE=1 SV=3 47 15 P01871 IGHM_HUMAN Ig mu chain C region OS=Homo sapiens GN=IGHM PE=1 SV=3 41 16 P04003 C4BPA_HUMAN C4b-binding protein alpha chain OS=Homo sapiens GN=C4BPA PE=1 SV=2 37 17 Q9Y6R7 FCGBP_HUMAN IgGFc-binding protein OS=Homo sapiens GN=FCGBP PE=1 SV=3 30 18 O43866 CD5L_HUMAN CD5 antigen-like OS=Homo -
POLR2I (F-11): Sc-398049
SANTA CRUZ BIOTECHNOLOGY, INC. POLR2I (F-11): sc-398049 BACKGROUND APPLICATIONS RNA polymerase II (Pol II) is a multi-subunit enzyme responsible for the tran- POLR2I (F-11) is recommended for detection of POLR2I of mouse, rat and scription of protein-coding genes. Transcription initiation requires recruitment human origin by Western Blotting (starting dilution 1:100, dilution range of the complete transcription machinery to a promoter via solicitation by 1:100-1:1000), immunoprecipitation [1-2 µg per 100-500 µg of total protein activators and chromatin remodeling factors. Pol II can coordinate 10 to 14 (1 ml of cell lysate)], immunofluorescence (starting dilution 1:50, dilution subunits. This complex interacts with the promoter regions of genes and a range 1:50-1:500), immunohistochemistry (including paraffin-embedded variety of elements and transcription factors. POLR2I (polymerase (RNA) II sections) (starting dilution 1:50, dilution range 1:50-1:500) and solid phase (DNA directed) polypeptide I), also known as RPB9 or hRPB14.5, is a 125 ELISA (starting dilution 1:30, dilution range 1:30-1:3000). amino acid nuclear protein belonging to the archaeal rpoM/eukaryotic RPA12/ POLR2I (F-11) is also recommended for detection of POLR2I in additional RPB9/RPC11 RNA polymerase family. Component of RNA polymerase II, POLR2I species, including equine, canine, bovine and porcine. catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. POLR2I is part of the upper jaw surrounding the Suitable for use as control antibody for POLR2I siRNA (h): sc-97881, POLR2I central large cleft and is thought to grab the incoming DNA template. -
ELOF1 Is a Transcription-Coupled DNA Repair Factor That Directs RNA Polymerase II Ubiquitylation
bioRxiv preprint doi: https://doi.org/10.1101/2021.02.25.432427; this version posted February 25, 2021. 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. 1 Van der Weegen et al. ELOF1 is a transcription-coupled DNA repair factor ELOF1 is a transcription-coupled DNA repair factor that directs RNA polymerase II ubiquitylation Yana van der Weegen1,*, Klaas de Lint2,*, Diana van den Heuvel1, Yuka Nakazawa3,4, Ishwarya 5 V. Narayanan5, Noud H.M. Klaassen1, Annelotte P. Wondergem1, Khashayar Roohollahi2, Janne J.M. van Schie2, Yuichiro Hara3,4, Mats Ljungman5,6, Tomoo Ogi3,4, Rob M.F. Wolthuis2,† , and Martijn S. Luijsterburg1,† Affiliations: 10 1 Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands 2 Cancer Center Amsterdam, Department of Clinical Genetics, Section Oncogenetics, Amsterdam University Medical Center, Amsterdam, the Netherlands 3 Department of Genetics, Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, Japan 15 4 Department of Human Genetics and Molecular Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan 5 Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA 6 Department of Environmental Health Sciences, Rogel Cancer Center and Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI, USA 20 †Correspondence to: [email protected] ; [email protected] Lead contact: [email protected] * These authors contributed equally to this work. bioRxiv preprint doi: https://doi.org/10.1101/2021.02.25.432427; this version posted February 25, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. -
Connectivity Analysis of Single-Cell RNA-Seq Derived Transcriptional
Connectivity analysis of single-cell RNA- seq derived transcriptional signatures A dissertation submitted to the Graduate School of the University of Cincinnati in partial fulfillment of the requirement for the degree of Doctor of Philosophy by Naim Al Mahi M.Sc. In Statistics, Ball State University, IN, 2014 B.Sc. In Statistics, University of Dhaka, Bangladesh, 2011 Committee Members: Mario Medvedovic, PhD (Chair) Jaroslaw Meller, PhD Siva Sivaganesan, PhD Jane Yu, PhD November 7, 2020 Division of Biostatistics and Bioinformatics Department of Environmental and Public Health Sciences University of Cincinnati College of Medicine Cincinnati, OH Abstract With the recent progress in high-throughput sequencing technologies, unprecedented amount of data from multiple omics modalities including genomics, transcriptomics, proteomics, and small-molecule data have become available. Accessibility and reusability of these biomedical big data provide immense opportunities and challenges as well. For example, integrating and connecting multiple data modalities such as, connecting single-cell transcriptomics data to small-molecule perturbational data can enhance the understanding of complex mechanisms underlie a disease and identify potential therapeutics. Recently released LINCS (Library of Integrated Network-based Cellular Signatures)-L1000 transcriptional signatures of chemical perturbations has opened new avenues to study cellular responses to existing drugs and new bioactive compounds. Connecting transcriptional signature of a disease to these chemical perturbation signatures to identify bioactive chemicals that can “revert” the disease signatures can lead to novel drug discovery and drug repurposing. Although, considerable research has been devoted to utilize bulk assay transcriptional data to study the relationship between diseases, genes, and drugs, considerably less attention has been paid to study the connection at the single cell level. -
Transcriptome Analysis of Adipose Tissues from Two Fat-Tailed Sheep
Li et al. BMC Genomics (2018) 19:338 https://doi.org/10.1186/s12864-018-4747-1 RESEARCHARTICLE Open Access Transcriptome analysis of adipose tissues from two fat-tailed sheep breeds reveals key genes involved in fat deposition Baojun Li1, Liying Qiao1, Lixia An2, Weiwei Wang1, Jianhua Liu1, Youshe Ren1, Yangyang Pan1, Jiongjie Jing1 and Wenzhong Liu1* Abstract Background: The level of fat deposition in carcass is a crucial factor influencing meat quality. Guangling Large-Tailed (GLT) and Small-Tailed Han (STH) sheep are important local Chinese fat-tailed breeds that show distinct patterns of fat depots. To gain a better understanding of fat deposition, transcriptome profiles were determined by RNA-sequencing of perirenal, subcutaneous, and tail fat tissues from both the sheep breeds. The common highly expressed genes (co-genes) in all the six tissues, and the genes that were differentially expressed (DE genes) between these two breeds in the corresponding tissues were analyzed. Results: Approximately 47 million clean reads were obtained for each sample, and a total of 17,267 genes were annotated. Of the 47 highly expressed co-genes, FABP4, ADIPOQ, FABP5,andCD36 were the four most highly transcribed genes among all the known genes related to adipose deposition. FHC, FHC-pseudogene,and ZC3H10 were also highly expressed genes and could, thus, have roles in fat deposition. A total of 2091, 4233, and 4131 DE genes were identified in the perirenal, subcutaneous, and tail fat tissues between the GLT and STH breeds, respectively. Gene Ontology (GO) analysis showed that some DE genes were associated with adipose metabolism. -
Comparative Transcriptome Profiling of Longissimus Muscle Tissues From
www.nature.com/scientificreports OPEN Comparative transcriptome profiling of longissimus muscle tissues from Qianhua Mutton Received: 29 April 2016 Accepted: 31 August 2016 Merino and Small Tail Han sheep Published: 20 September 2016 Limin Sun, Man Bai, Lujie Xiang, Guishan Zhang, Wei Ma & Huaizhi Jiang The Qianhua Mutton Merino (QHMM) is a new sheep (Ovis aries) variety with better meat performance compared with the traditional local variety Small Tail Han (STH) sheep. We aimed to evaluate the transcriptome regulators associated with muscle growth and development between the QHMM and STH. We used RNA-Seq to obtain the transcriptome profiles of the longissimus muscle from the QHMM and STH. The results showed that 960 genes were differentially expressed (405 were up- regulated and 555 were down-regulated). Among these, 463 differently expressed genes (DEGs) were probably associated with muscle growth and development and were involved in biological processes such as skeletal muscle tissue development and muscle cell differentiation; molecular functions such as catalytic activity and oxidoreductase activity; cellular components such as mitochondrion and sarcoplasmic reticulum; and pathways such as metabolic pathways and citrate cycle. From the potential genes, a gene-act-network and co-expression-network closely related to muscle growth and development were identified and established. Finally, the expressions of nine genes were validated by real-time PCR. The results suggested that some DEGs, including MRFs, GXP1 and STAC3, play crucial roles in muscle growth and development processes. This genome-wide transcriptome analysis of QHMM and STH muscle is reported for the first time. Sheep (Ovis aries) form a large part of the global animal husbandry industry. -
A Chromosome-Centric Human Proteome Project (C-HPP) To
computational proteomics Laboratory for Computational Proteomics www.FenyoLab.org E-mail: [email protected] Facebook: NYUMC Computational Proteomics Laboratory Twitter: @CompProteomics Perspective pubs.acs.org/jpr A Chromosome-centric Human Proteome Project (C-HPP) to Characterize the Sets of Proteins Encoded in Chromosome 17 † ‡ § ∥ ‡ ⊥ Suli Liu, Hogune Im, Amos Bairoch, Massimo Cristofanilli, Rui Chen, Eric W. Deutsch, # ¶ △ ● § † Stephen Dalton, David Fenyo, Susan Fanayan,$ Chris Gates, , Pascale Gaudet, Marina Hincapie, ○ ■ △ ⬡ ‡ ⊥ ⬢ Samir Hanash, Hoguen Kim, Seul-Ki Jeong, Emma Lundberg, George Mias, Rajasree Menon, , ∥ □ △ # ⬡ ▲ † Zhaomei Mu, Edouard Nice, Young-Ki Paik, , Mathias Uhlen, Lance Wells, Shiaw-Lin Wu, † † † ‡ ⊥ ⬢ ⬡ Fangfei Yan, Fan Zhang, Yue Zhang, Michael Snyder, Gilbert S. Omenn, , Ronald C. Beavis, † # and William S. Hancock*, ,$, † Barnett Institute and Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States ‡ Stanford University, Palo Alto, California, United States § Swiss Institute of Bioinformatics (SIB) and University of Geneva, Geneva, Switzerland ∥ Fox Chase Cancer Center, Philadelphia, Pennsylvania, United States ⊥ Institute for System Biology, Seattle, Washington, United States ¶ School of Medicine, New York University, New York, United States $Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia ○ MD Anderson Cancer Center, Houston, Texas, United States ■ Yonsei University College of Medicine, Yonsei University, -
CREB-Dependent Transcription in Astrocytes: Signalling Pathways, Gene Profiles and Neuroprotective Role in Brain Injury
CREB-dependent transcription in astrocytes: signalling pathways, gene profiles and neuroprotective role in brain injury. Tesis doctoral Luis Pardo Fernández Bellaterra, Septiembre 2015 Instituto de Neurociencias Departamento de Bioquímica i Biologia Molecular Unidad de Bioquímica y Biologia Molecular Facultad de Medicina CREB-dependent transcription in astrocytes: signalling pathways, gene profiles and neuroprotective role in brain injury. Memoria del trabajo experimental para optar al grado de doctor, correspondiente al Programa de Doctorado en Neurociencias del Instituto de Neurociencias de la Universidad Autónoma de Barcelona, llevado a cabo por Luis Pardo Fernández bajo la dirección de la Dra. Elena Galea Rodríguez de Velasco y la Dra. Roser Masgrau Juanola, en el Instituto de Neurociencias de la Universidad Autónoma de Barcelona. Doctorando Directoras de tesis Luis Pardo Fernández Dra. Elena Galea Dra. Roser Masgrau In memoriam María Dolores Álvarez Durán Abuela, eres la culpable de que haya decidido recorrer el camino de la ciencia. Que estas líneas ayuden a conservar tu recuerdo. A mis padres y hermanos, A Meri INDEX I Summary 1 II Introduction 3 1 Astrocytes: physiology and pathology 5 1.1 Anatomical organization 6 1.2 Origins and heterogeneity 6 1.3 Astrocyte functions 8 1.3.1 Developmental functions 8 1.3.2 Neurovascular functions 9 1.3.3 Metabolic support 11 1.3.4 Homeostatic functions 13 1.3.5 Antioxidant functions 15 1.3.6 Signalling functions 15 1.4 Astrocytes in brain pathology 20 1.5 Reactive astrogliosis 22 2 The transcription