Regions of Homozygosity Identified by SNP Microarray Analysis Aid in The
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ACOX3 Antibody
Product Datasheet ACOX3 antibody Catalog No: #22136 Orders: [email protected] Description Support: [email protected] Product Name ACOX3 antibody Host Species Rabbit Clonality Polyclonal Purification Purified by antigen-affinity chromatography. Applications WB IHC Species Reactivity Hu Immunogen Type Recombinant protein Immunogen Description Recombinant protein fragment contain a sequence corresponding to a region within amino acids 408 and 613 of ACOX3 Target Name ACOX3 Accession No. Swiss-Prot:O15254Gene ID:8310 Concentration 1mg/ml Formulation Supplied in 0.1M Tris-buffered saline with 20% Glycerol (pH7.0). 0.01% Thimerosal was added as a preservative. Storage Store at -20°C for long term preservation (recommended). Store at 4°C for short term use. Application Details Predicted MW: 70kd Western blotting: 1:500-1:3000 Immunohistochemistry: 1:100-1:500 Images Sample (30 ug of whole cell lysate) A: A549 7.5% SDS PAGE Primary antibody diluted at 1: 1000 Address: 8400 Baltimore Ave., Suite 302, College Park, MD 20740, USA http://www.sabbiotech.com 1 Immunohistochemical analysis of paraffin-embedded H441 xenograft, using ACOX3 antibody at 1: 500 dilution. Background Acyl-Coenzyme A oxidase 3 also know as pristanoyl -CoA oxidase (ACOX3)is involved in the desaturation of 2-methyl branched fatty acids in peroxisomes. Unlike the rat homolog, the human gene is expressed in very low amounts in liver such that its mRNA was undetectable by routine Northern-blot analysis or its product by immunoblotting or by enzyme activity measurements. However the human cDNA encoding a 700 amino acid protein with a peroxisomal targeting C-terminal tripeptide S-K-L was isolated and is thought to be expressed under special conditions such as specific developmental stages or in a tissue specific manner in tissues that have not yet been examined. -
ACOX3 Human Shrna Plasmid Kit (Locus ID 8310) Product Data
OriGene Technologies, Inc. 9620 Medical Center Drive, Ste 200 Rockville, MD 20850, US Phone: +1-888-267-4436 [email protected] EU: [email protected] CN: [email protected] Product datasheet for TL314988 ACOX3 Human shRNA Plasmid Kit (Locus ID 8310) Product data: Product Type: shRNA Plasmids Product Name: ACOX3 Human shRNA Plasmid Kit (Locus ID 8310) Locus ID: 8310 Vector: pGFP-C-shLenti (TR30023) Format: Lentiviral plasmids Components: ACOX3 - Human, 4 unique 29mer shRNA constructs in lentiviral GFP vector(Gene ID = 8310). 5µg purified plasmid DNA per construct Non-effective 29-mer scrambled shRNA cassette in pGFP-C-shLenti Vector, TR30021, included for free. RefSeq: NM_001101667, NM_003501, NM_003501.1, NM_003501.2, NM_001101667.1, BC017053, NM_003501.3, NM_001101667.2 Summary: Acyl-Coenzyme A oxidase 3 also know as pristanoyl -CoA oxidase (ACOX3)is involved in the desaturation of 2-methyl branched fatty acids in peroxisomes. Unlike the rat homolog, the human gene is expressed in very low amounts in liver such that its mRNA was undetectable by routine Northern-blot analysis or its product by immunoblotting or by enzyme activity measurements. However the human cDNA encoding a 700 amino acid protein with a peroxisomal targeting C-terminal tripeptide S-K-L was isolated and is thought to be expressed under special conditions such as specific developmental stages or in a tissue specific manner in tissues that have not yet been examined. [provided by RefSeq, Jul 2008] shRNA Design: These shRNA constructs were designed against multiple splice variants at this gene locus. To be certain that your variant of interest is targeted, please contact [email protected]. -
ACOX3 (H-1): Sc-390624
SAN TA C RUZ BI OTEC HNOL OG Y, INC . ACOX3 (H-1): sc-390624 BACKGROUND APPLICATIONS ACOX3 (acyl-Coenzyme A oxidase 3), also known as BRCOX or PRCOX, is a ACOX3 (H-1) is recommended for detection of ACOX3 of mouse, rat and 700 amino acid protein that localizes to peroxisomes and belongs to the acyl- human origin by Western Blotting (starting dilution 1:100, dilution range CoA oxidase family. Using FAD as a cofactor, ACOX3 catalyzes the desatura - 1:100-1:1000), immunoprecipitation [1-2 µg per 100-500 µg of total protein tion of 2-methyl branched fatty acids in peroxisomes, thereby playing an impor - (1 ml of cell lysate)], immunofluorescence (starting dilution 1:50, dilution tant role in peroxisomal fatty acid β-oxidation. Human ACOX3 shares 75% range 1:50-1:500) and solid phase ELISA (starting dilution 1:30, dilution sequence identity with its rat counterpart, suggesting a conserved role range 1:30-1:3000). between species. Multiple isoforms of ACOX3 exist due to alternative splic - Suitable for use as control antibody for ACOX3 siRNA (h): sc-89236, ACOX3 ing events. The gene encoding ACOX3 maps to human chromosome 4, which siRNA (m): sc-140819, ACOX3 shRNA Plasmid (h): sc-89236-SH, ACOX3 encodes nearly 6% of the human genome and has the largest gene deserts shRNA Plasmid (m): sc-140819-SH, ACOX3 shRNA (h) Lentiviral Particles: (regions of the genome with no protein encoding genes) of all of the human sc-89236-V and ACOX3 shRNA (m) Lentiviral Particles: sc-140819-V. chromosomes. Defects in some of the genes located on chromosome 4 are associated with Huntington’s disease, Ellis-van Creveld syndrome, methyl - Molecular Weight of ACOX3: 78 kDa. -
Genome-Wide Human SNP Array 6.0
Data Sheet Genome-Wide Human SNP Array 6.0 Introduction The Genome-Wide Human SNP Array 6.0 contains more than 906,600 single nucleotide polymorphisms (SNPs) and more than 946,000 probes for the detection of copy number variation. SNPs on the array are present on 200 to 1,100 base pairs (bp) Nsp I or Sty I digested fragments in the human genome, and are amplified using the Genome-Wide Human SNP Nsp/Sty Assay Kit 5.0/6.0. This assay, which is also compatible with the SNP Array 5.0, now combines the Nsp and Sty fractions previously assayed on two separate arrays. SNPs on the SNP Array 6.0 were screened in more than 500 distinct samples, including 270 HapMap samples and separate diversity samples. Approximately 482,000 SNPs are derived from the previous-generation Mapping 500K and SNP 5.0 Arrays. The remaining 424,000 SNPs include tag SNP markers derived from the International HapMap Project. These novel markers have better representation of SNPs on chromosomes X and Y, mitochondrial SNPs, SNPs in recombination hotspots, and new SNPs added to the dbSNP database after completion of the GeneChip® Human Mapping 500K Array Set. This array contains a total of 946,000 non-polymorphic copy number probes. These probes—744,000 originally selected for their spacing and 202,000 selected based on known copy number changes reported in the Toronto Database of Genomic Variants (DGV)—enable you to detect de novo copy number changes and perform association studies by genotyping both SNP and known copy number polymorphism (CNP) loci (as The Genome-Wide Human SNP Array 6.0 reported by McCarroll, et al.). -
Novel and Highly Recurrent Chromosomal Alterations in Se´Zary Syndrome
Research Article Novel and Highly Recurrent Chromosomal Alterations in Se´zary Syndrome Maarten H. Vermeer,1 Remco van Doorn,1 Remco Dijkman,1 Xin Mao,3 Sean Whittaker,3 Pieter C. van Voorst Vader,4 Marie-Jeanne P. Gerritsen,5 Marie-Louise Geerts,6 Sylke Gellrich,7 Ola So¨derberg,8 Karl-Johan Leuchowius,8 Ulf Landegren,8 Jacoba J. Out-Luiting,1 Jeroen Knijnenburg,2 Marije IJszenga,2 Karoly Szuhai,2 Rein Willemze,1 and Cornelis P. Tensen1 Departments of 1Dermatology and 2Molecular Cell Biology, Leiden University Medical Center, Leiden, the Netherlands; 3Department of Dermatology, St Thomas’ Hospital, King’s College, London, United Kingdom; 4Department of Dermatology, University Medical Center Groningen, Groningen, the Netherlands; 5Department of Dermatology, Radboud University Nijmegen Medical Center, Nijmegen, the Netherlands; 6Department of Dermatology, Gent University Hospital, Gent, Belgium; 7Department of Dermatology, Charite, Berlin, Germany; and 8Department of Genetics and Pathology, Rudbeck Laboratory, University of Uppsala, Uppsala, Sweden Abstract Introduction This study was designed to identify highly recurrent genetic Se´zary syndrome (Sz) is an aggressive type of cutaneous T-cell alterations typical of Se´zary syndrome (Sz), an aggressive lymphoma/leukemia of skin-homing, CD4+ memory T cells and is cutaneous T-cell lymphoma/leukemia, possibly revealing characterized by erythroderma, generalized lymphadenopathy, and pathogenetic mechanisms and novel therapeutic targets. the presence of neoplastic T cells (Se´zary cells) in the skin, lymph High-resolution array-based comparative genomic hybridiza- nodes, and peripheral blood (1). Sz has a poor prognosis, with a tion was done on malignant T cells from 20 patients. disease-specific 5-year survival of f24% (1). -
An Integrated Map of Genetic Variation from 1,092 Human Genomes
ARTICLE doi:10.1038/nature11632 An integrated map of genetic variation from 1,092 human genomes The 1000 Genomes Project Consortium* By characterizing the geographic and functional spectrum of human genetic variation, the 1000 Genomes Project aims to build a resource to help to understand the genetic contribution to disease. Here we describe the genomes of 1,092 individuals from 14 populations, constructed using a combination of low-coverage whole-genome and exome sequencing. By developing methods to integrate information across several algorithms and diverse data sources, we provide a validated haplotype map of 38 million single nucleotide polymorphisms, 1.4 million short insertions and deletions, and more than 14,000 larger deletions. We show that individuals from different populations carry different profiles of rare and common variants, and that low-frequency variants show substantial geographic differentiation, which is further increased by the action of purifying selection. We show that evolutionary conservation and coding consequence are key determinants of the strength of purifying selection, that rare-variant load varies substantially across biological pathways, and that each individual contains hundreds of rare non-coding variants at conserved sites, such as motif-disrupting changes in transcription-factor-binding sites. This resource, which captures up to 98% of accessible single nucleotide polymorphisms at a frequency of 1% in related populations, enables analysis of common and low-frequency variants in individuals from diverse, including admixed, populations. Recent efforts to map human genetic variation by sequencing exomes1 individual genome sequences, to help separate shared variants from and whole genomes2–4 have characterized the vast majority of com- those private to families, for example. -
Chromosome SNP Microarray a New High-Density Allele-Specific Diagnostic Platform
Chromosome SNP Microarray A New High-density Allele-specific Diagnostic Platform Analysis of submicroscopic genomic changes can pair (allele) targets that have two different forms, revealing which form is present at that locus as well as the number of copies of that detect the cause of congenital anomalies and/or DNA segment. CGH-based arrays cannot detect polymorphic allele learning disabilities. targets (only dosage), resulting in a significant advantage for the SNP array. This advantage is based both on added confirmation of Introduction dosage changes through allele comparisons and the identification of Genetic imbalances are often associated with multiple birth defects, syndrome-associated “copy neutral” contiguous stretches of allele developmental delay, growth retardation, and dysmorphic features. homozygosity. The presence of the latter allows for detection of Standard cytogenetic analysis can identify visible chromosomal uniparental disomy for all chromosomes and, when consanguinity alterations, such as an extra chromosome band, but small deletions is present, it will provide the degree as well as the resulting genomic or duplications in the genome cannot be reliably detected. location of regions of recessive allele risk.5,6 Submicroscopic unbalanced rearrangements have been found in approximately 3% of patients with learning disabilities and mental Increase in Genomic Targets retardation of unknown cause using a set of FISH (fluorescence The initial 262,000 SNP microarray has been upgraded to offer a in situ hybridization) probes that can only target the ends of the much more dense array of 1.8 million genomic targets (marker every chromosomes.1 700 bp).7 The ultra dense array is much more sensitive in identifying extremely small genomic variations and more statistically reliable Advances in molecular cytogenetics further improved the sensitivity due to the large increase in markers through which each variation is of testing through the application of microarray-based comparative detected. -
Identity-By-Descent Detection Across 487,409 British Samples Reveals Fine Scale Population Structure and Ultra-Rare Variant Asso
ARTICLE https://doi.org/10.1038/s41467-020-19588-x OPEN Identity-by-descent detection across 487,409 British samples reveals fine scale population structure and ultra-rare variant associations ✉ Juba Nait Saada 1 , Georgios Kalantzis 1, Derek Shyr 2, Fergus Cooper 3, Martin Robinson 3, ✉ Alexander Gusev 4,5,7 & Pier Francesco Palamara 1,6,7 1234567890():,; Detection of Identical-By-Descent (IBD) segments provides a fundamental measure of genetic relatedness and plays a key role in a wide range of analyses. We develop FastSMC, an IBD detection algorithm that combines a fast heuristic search with accurate coalescent-based likelihood calculations. FastSMC enables biobank-scale detection and dating of IBD segments within several thousands of years in the past. We apply FastSMC to 487,409 UK Biobank samples and detect ~214 billion IBD segments transmitted by shared ancestors within the past 1500 years, obtaining a fine-grained picture of genetic relatedness in the UK. Sharing of common ancestors strongly correlates with geographic distance, enabling the use of genomic data to localize a sample’s birth coordinates with a median error of 45 km. We seek evidence of recent positive selection by identifying loci with unusually strong shared ancestry and detect 12 genome-wide significant signals. We devise an IBD-based test for association between phenotype and ultra-rare loss-of-function variation, identifying 29 association sig- nals in 7 blood-related traits. 1 Department of Statistics, University of Oxford, Oxford, UK. 2 Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA. 3 Department of Computer Science, University of Oxford, Oxford, UK. -
Genetic Profiles of 103,106 Individuals in the Taiwan Biobank Provide Insights Into the Health and History of Han Chinese
UCSF UC San Francisco Previously Published Works Title Genetic profiles of 103,106 individuals in the Taiwan Biobank provide insights into the health and history of Han Chinese. Permalink https://escholarship.org/uc/item/9s81s8g7 Journal NPJ genomic medicine, 6(1) ISSN 2056-7944 Authors Wei, Chun-Yu Yang, Jenn-Hwai Yeh, Erh-Chan et al. Publication Date 2021-02-11 DOI 10.1038/s41525-021-00178-9 Peer reviewed eScholarship.org Powered by the California Digital Library University of California www.nature.com/npjgenmed ARTICLE OPEN Genetic profiles of 103,106 individuals in the Taiwan Biobank provide insights into the health and history of Han Chinese Chun-Yu Wei1,4, Jenn-Hwai Yang1,4, Erh-Chan Yeh1, Ming-Fang Tsai1, Hsiao-Jung Kao1, Chen-Zen Lo1, Lung-Pao Chang1, Wan-Jia Lin1, Feng-Jen Hsieh1, Saurabh Belsare 2, Anand Bhaskar 3, Ming-Wei Su1, Te-Chang Lee1, Yi-Ling Lin1, Fu-Tong Liu1, Chen-Yang Shen1, ✉ Ling-Hui Li1, Chien-Hsiun Chen1, Jeffrey D. Wall2, Jer-Yuarn Wu1 and Pui-Yan Kwok 1,2 Personalized medical care focuses on prediction of disease risk and response to medications. To build the risk models, access to both large-scale genomic resources and human genetic studies is required. The Taiwan Biobank (TWB) has generated high- coverage, whole-genome sequencing data from 1492 individuals and genome-wide SNP data from 103,106 individuals of Han Chinese ancestry using custom SNP arrays. Principal components analysis of the genotyping data showed that the full range of Han Chinese genetic variation was found in the cohort. -
SNP Ascertainment Bias in Population Genetic Analyses: Why It Is Important, and How to Correct It Recently in Press
Prospects & Overviews SNP ascertainment bias in population genetic analyses: Why it is important, and how to correct it Recently in press Joseph Lachanceà and Sarah A. Tishkoff Whole genome sequencing and SNP genotyping arrays African hunter-gatherers and the power can paint strikingly different pictures of demographic of whole genome sequencing history and natural selection. This is because genotyping arrays contain biased sets of pre-ascertained SNPs. In this Due to technological advances and increases in computation- al power, the cost of genotyping has plummeted over the past short review, we use comparisons between high-coverage few years. Because of this, it is now feasible to conduct whole genome sequences of African hunter-gatherers and population genetic analyses of whole genome sequencing data from genotyping arrays to highlight how SNP data. One advantage of whole genome sequencing is that ascertainment bias distorts population genetic inferences. SNP ascertainment bias is reduced compared to alternative Sample sizes and the populations in which SNPs are genotyping technologies. This lack of SNP ascertainment bias discovered affect the characteristics of observed variants. is critical for accurate population genetic analyses where allele frequency distributions are used to infer demographic We find that SNPs on genotyping arrays tend to be older history and scan for past targets of natural selection. Using the and present in multiple populations. In addition, geno- technology of Complete Genomics [1], we recently sequenced typing arrays cause allele frequency distributions to be the whole genomes of 15 African hunter-gatherers at >60 shifted towards intermediate frequency alleles, and coverage [2]. Sequenced individuals included five Pygmies estimates of linkage disequilibrium are modified. -
Downloaded from Ftp://Ftp.Uniprot.Org/ on July 3, 2019) Using Maxquant (V1.6.10.43) Search Algorithm
bioRxiv preprint doi: https://doi.org/10.1101/2020.11.17.385096; this version posted November 17, 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. The proteomic landscape of resting and activated CD4+ T cells reveal insights into cell differentiation and function Yashwanth Subbannayya1, Markus Haug1, Sneha M. Pinto1, Varshasnata Mohanty2, Hany Zakaria Meås1, Trude Helen Flo1, T.S. Keshava Prasad2 and Richard K. Kandasamy1,* 1Centre of Molecular Inflammation Research (CEMIR), and Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, N-7491 Trondheim, Norway 2Center for Systems Biology and Molecular Medicine, Yenepoya (Deemed to be University), Mangalore, India *Correspondence to: Professor Richard Kumaran Kandasamy Norwegian University of Science and Technology (NTNU) Centre of Molecular Inflammation Research (CEMIR) PO Box 8905 MTFS Trondheim 7491 Norway E-mail: [email protected] (Kandasamy R K) Tel.: +47-7282-4511 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.11.17.385096; this version posted November 17, 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 CD4+ T cells (T helper cells) are cytokine-producing adaptive immune cells that activate or regulate the responses of various immune cells. -
Mutagenesys: Estimating Individual Disease Susceptibility Based On
Vol. 24 no. 3 2008, pages 440–442 BIOINFORMATICS APPLICATIONS NOTE doi:10.1093/bioinformatics/btm587 Databases and ontologies MutaGeneSys: estimating individual disease susceptibility based on genome-wide SNP array data Julia Stoyanovich* and Itsik Pe’er Department of Computer Science, Columbia University, 1214 Amsterdam Avenue, New York, NY 10025, USA Received on May 29, 2007; revised on October 16, 2007; accepted on November 22, 2007 Advance Access publication November 29, 2007 Associate Editor: Jonathan Wren ABSTRACT First and foremost, genetic information remains expensive Summary: We present MutaGeneSys: a system that uses genome- to collect, and it is currently economically prohibitive to wide genotype data to estimate disease susceptibility. Our system make a complete set of an individual’s genotypes of SNPs integrates three data sources: the International HapMap project, available for analysis. Nature Genetics’ ‘Question of the Year’ whole-genome marker correlation data and the Online Mendelian (www.nature.com/ng/qoty) announced the sequencing of the Inheritance in Man (OMIM) database. It accepts SNP data of indivi- entire human genome for $1000 as a goal for the genetics duals as query input and delivers disease susceptibility hypotheses community. Cost-effective methods (e.g. SNP arrays) currently even if the original set of typed SNPs is incomplete. Our system exist for collecting genetic data from 1% to 5% of all 11 million is scalable and flexible: it produces population, technology and human SNPs. This calls for the development of techniques that confidence-specific predictions in interactive time. can effectively utilize partial genetic information for disease Availability: Our system is available as an online resource at http:// prediction.