DOCSLIB.ORG

Mouse Thap2 Conditional Knockout Project (CRISPR/Cas9)

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Mouse Thap2 Conditional Knockout Project (CRISPR/Cas9) https://www.alphaknockout.com Mouse Thap2 Conditional Knockout Project (CRISPR/Cas9) Objective: To create a Thap2 conditional knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering. Strategy summary: The Thap2 gene (NCBI Reference Sequence: NM_025780 ; Ensembl: ENSMUSG00000020137 ) is located on Mouse chromosome 10. 3 exons are identified, with the ATG start codon in exon 1 and the TAA stop codon in exon 3 (Transcript: ENSMUST00000218842). Exon 3 will be selected as conditional knockout region (cKO region). Deletion of this region should result in the loss of function of the Mouse Thap2 gene. To engineer the targeting vector, homologous arms and cKO region will be generated by PCR using BAC clone RP23-145J21 as template. Cas9, gRNA and targeting vector will be co-injected into fertilized eggs for cKO Mouse production. The pups will be genotyped by PCR followed by sequencing analysis. Note: Exon 3 covers 58.99% of the coding region. Start codon is in exon 1, and stop codon is in exon 3. The size of intron 2 for 5'-loxP site insertion: 3405 bp. The size of effective cKO region: ~657 bp. The cKO region does not have any other known gene. Page 1 of 7 https://www.alphaknockout.com Overview of the Targeting Strategy gRNA region Wildtype allele T A 5' gRNA region A 3' 1 3 Targeting vector T A A Targeted allele T A A Constitutive KO allele (After Cre recombination) Legends Exon of mouse Thap2 Homology arm cKO region loxP site Page 2 of 7 https://www.alphaknockout.com Overview of the Dot Plot Window size: 10 bp Forward Reverse Complement Sequence 12 Note: The sequence of homologous arms and cKO region 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 GC Content Distribution Window size: 300 bp Sequence 12 Summary: Full Length(6884bp) | A(30.68% 2112) | C(19.8% 1363) | T(29.13% 2005) | G(20.4% 1404) Note: The sequence of homologous arms and cKO region is analyzed to determine the GC content. No significant high GC-content region is found. So this region is suitable for PCR screening or sequencing analysis. Page 3 of 7 https://www.alphaknockout.com BLAT Search Results (up) QUERY SCORE START END QSIZE IDENTITY CHROM STRAND START END SPAN -------------------------------------------------------------------------------------------------------------- browser details YourSeq 3000 1 3000 3000 100.0% chr10 - 115373197 115376196 3000 browser details YourSeq 303 1343 1725 3000 94.3% chr10 - 41143455 41144004 550 browser details YourSeq 303 1395 1735 3000 95.1% chr13 + 101282054 101282414 361 browser details YourSeq 299 1398 1724 3000 96.1% chr1 - 156176682 156177026 345 browser details YourSeq 297 1398 1726 3000 95.5% chr6 - 82451150 82451496 347 browser details YourSeq 296 1398 1724 3000 95.8% chr6 + 50511813 50554375 42563 browser details YourSeq 295 1397 1724 3000 95.5% chr1 + 142083910 142084256 347 browser details YourSeq 293 1396 1725 3000 94.9% chr14 + 35128844 35129192 349 browser details YourSeq 291 1400 1725 3000 95.4% chr12 - 99863475 99863818 344 browser details YourSeq 289 1398 1734 3000 94.5% chr1 - 153751081 153751441 361 browser details YourSeq 285 1393 1724 3000 94.5% chr3 + 130849586 130849937 352 browser details YourSeq 284 1398 1725 3000 94.7% chr19 - 49872226 49872572 347 browser details YourSeq 284 1398 1724 3000 95.3% chr6 + 49568447 49568778 332 browser details YourSeq 283 1397 1724 3000 95.4% chr5 - 36409575 36409897 323 browser details YourSeq 283 1394 1729 3000 94.7% chr14 + 118811229 118811566 338 browser details YourSeq 281 1126 1724 3000 91.0% chr3 + 51351672 51352199 528 browser details YourSeq 280 1397 1724 3000 94.1% chr7 - 23144900 23145246 347 browser details YourSeq 280 1397 1724 3000 94.1% chr7 - 21921711 21922057 347 browser details YourSeq 280 1398 1724 3000 96.1% chr4 - 121204688 121205014 327 browser details YourSeq 280 1397 1724 3000 94.1% chr16 - 54634337 54634683 347 Note: The 3000 bp section upstream of Exon 3 is BLAT searched against the genome. No significant similarity is found. BLAT Search Results (down) QUERY SCORE START END QSIZE IDENTITY CHROM STRAND START END SPAN ----------------------------------------------------------------------------------------------- browser details YourSeq 3000 1 3000 3000 100.0% chr10 - 115369563 115372562 3000 browser details YourSeq 150 495 1153 3000 83.6% chr16 + 35613421 35613590 170 browser details YourSeq 145 895 1429 3000 92.4% chr8 - 110794676 110795218 543 browser details YourSeq 144 486 1148 3000 82.2% chr10 + 128747227 128747415 189 browser details YourSeq 138 927 1156 3000 93.7% chr4 - 126561012 126561328 317 browser details YourSeq 138 891 1144 3000 95.4% chr18 + 36708158 36709500 1343 browser details YourSeq 135 891 1157 3000 85.4% chr11 + 95134678 95134833 156 browser details YourSeq 134 913 1157 3000 96.6% chr4 + 116885798 116886247 450 browser details YourSeq 134 889 1132 3000 89.0% chr16 + 11235959 11236471 513 browser details YourSeq 134 924 1171 3000 93.0% chr1 + 179170208 179467375 297168 browser details YourSeq 132 894 1168 3000 92.3% chr12 + 4363697 4363996 300 browser details YourSeq 130 891 1157 3000 84.4% chr19 - 46048717 46048871 155 browser details YourSeq 128 893 1156 3000 84.1% chr14 - 121240851 121240995 145 browser details YourSeq 128 498 1157 3000 79.9% chr4 + 125999535 125999699 165 browser details YourSeq 127 891 1153 3000 84.2% chr5 + 25027338 25027489 152 browser details YourSeq 127 924 1172 3000 85.2% chr2 + 84699858 84700009 152 browser details YourSeq 126 494 1147 3000 80.5% chr4 + 150718674 150718819 146 browser details YourSeq 125 891 1157 3000 82.9% chr11 - 98989084 98989238 155 browser details YourSeq 125 486 1135 3000 79.9% chr16 + 55587015 55587166 152 browser details YourSeq 124 891 1153 3000 85.2% chr18 - 36583831 36583979 149 Note: The 3000 bp section downstream of Exon 3 is BLAT searched against the genome. No significant similarity is found. Page 4 of 7 https://www.alphaknockout.com Gene and protein information: Thap2 THAP domain containing, apoptosis associated protein 2 [ Mus musculus (house mouse) ] Gene ID: 66816, updated on 12-Aug-2019 Gene summary Official Symbol Thap2 provided by MGI Official Full Name THAP domain containing, apoptosis associated protein 2 provided by MGI Primary source MGI:MGI:1914066 See related Ensembl:ENSMUSG00000020137 Gene type protein coding RefSeq status VALIDATED Organism Mus musculus Lineage Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus Also known as AI450385; AI649097; 2900040O07Rik; 9030625G08Rik Expression Ubiquitous expression in whole brain E14.5 (RPKM 5.3), CNS E11.5 (RPKM 4.9) and 28 other tissues See more Orthologs human all Genomic context Location: 10; 10 D2 See Thap2 in Genome Data Viewer Exon count: 3 Annotation release Status Assembly Chr Location 108 current GRCm38.p6 (GCF_000001635.26) 10 NC_000076.6 (115368398..115384435, complement) Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 10 NC_000076.5 (114807022..114821491, complement) Chromosome 10 - NC_000076.6 Page 5 of 7 https://www.alphaknockout.com Transcript information: This gene has 3 transcripts Gene: Thap2 ENSMUSG00000020137 Description THAP domain containing, apoptosis associated protein 2 [Source:MGI Symbol;Acc:MGI:1914066] Gene Synonyms 2900040O07Rik, 9030625G08Rik Location Chromosome 10: 115,368,404-115,384,443 reverse strand. GRCm38:CM001003.2 About this gene This gene has 3 transcripts (splice variants), 181 orthologues, 5 paralogues and is a member of 1 Ensembl protein family. Transcripts Name Transcript ID bp Protein Translation ID Biotype CCDS UniProt Flags Thap2-202 ENSMUST00000218842.1 4970 217aa ENSMUSP00000151353.1 Protein coding CCDS24179 Q9D305 TSL:1 GENCODE basic APPRIS P1 Thap2-201 ENSMUST00000020346.5 3681 49aa ENSMUSP00000020346.5 Protein coding - A0A1X7SB55 TSL:1 GENCODE basic Thap2-203 ENSMUST00000218989.1 527 37aa ENSMUSP00000151925.1 Protein coding - A0A1W2P852 TSL:NA GENCODE basic 36.04 kb Forward strand 115.36Mb 115.37Mb 115.38Mb 115.39Mb Genes Zfc3h1-201 >protein coding (Comprehensive set... Contigs AC126943.5 > Genes (Comprehensive set... < Tmem19-206protein coding < Thap2-202protein coding < Tmem19-203protein coding < Thap2-201protein coding < Tmem19-201protein coding < Thap2-203protein coding < Tmem19-204protein coding < Tmem19-209protein coding < Tmem19-202protein coding < Tmem19-210protein coding < Tmem19-205lncRNA < Tmem19-207retained intron Regulatory Build 115.36Mb 115.37Mb 115.38Mb 115.39Mb Reverse strand 36.04 kb Regulation Legend CTCF Enhancer Open Chromatin Promoter Promoter Flank Gene Legend Protein Coding Ensembl protein coding merged Ensembl/Havana Non-Protein Coding processed transcript RNA gene Page 6 of 7 https://www.alphaknockout.com Transcript: ENSMUST00000218842 < Thap2-202protein coding Reverse strand 16.03 kb ENSMUSP00000151... Low complexity (Seg) Coiled-coils (Ncoils) Superfamily SSF57716 SMART THAP-type zinc finger THAP-type zinc finger Pfam THAP-type zinc finger PROSITE profiles THAP-type zinc finger PANTHER THAP domain-containing protein 2 Gene3D THAP-type zinc finger superfamily All sequence SNPs/i... Sequence variants (dbSNP and all other sources) Variant Legend stop gained missense variant synonymous variant Scale bar 0 20 40 60 80 100 120 140 160 180 217 We wish to acknowledge the following valuable scientific information resources: Ensembl, MGI, NCBI, UCSC. Page 7 of 7.
Load more

Recommended publications
  • Replace This with the Actual Title Using All Caps
    UNDERSTANDING THE GENETICS UNDERLYING MASTITIS USING A MULTI-PRONGED APPROACH A Dissertation Presented to the Faculty of the Graduate School of Cornell University In Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy by Asha Marie Miles December 2019 © 2019 Asha Marie Miles UNDERSTANDING THE GENETICS UNDERLYING MASTITIS USING A MULTI-PRONGED APPROACH Asha Marie Miles, Ph. D. Cornell University 2019 This dissertation addresses deficiencies in the existing genetic characterization of mastitis due to granddaughter study designs and selection strategies based primarily on lactation average somatic cell score (SCS). Composite milk samples were collected across 6 sampling periods representing key lactation stages: 0-1 day in milk (DIM), 3- 5 DIM, 10-14 DIM, 50-60 DIM, 90-110 DIM, and 210-230 DIM. Cows were scored for front and rear teat length, width, end shape, and placement, fore udder attachment, udder cleft, udder depth, rear udder height, and rear udder width. Independent multivariable logistic regression models were used to generate odds ratios for elevated SCC (≥ 200,000 cells/ml) and farm-diagnosed clinical mastitis. Within our study cohort, loose fore udder attachment, flat teat ends, low rear udder height, and wide rear teats were associated with increased odds of mastitis. Principal component analysis was performed on these traits to create a single new phenotype describing mastitis susceptibility based on these high-risk phenotypes. Cows (N = 471) were genotyped on the Illumina BovineHD 777K SNP chip and considering all 14 traits of interest, a total of 56 genome-wide associations (GWA) were performed and 28 significantly associated quantitative trait loci (QTL) were identified.
    [Show full text]
  • Environmental Influences on Endothelial Gene Expression
    ENDOTHELIAL CELL GENE EXPRESSION John Matthew Jeff Herbert Supervisors: Prof. Roy Bicknell and Dr. Victoria Heath PhD thesis University of Birmingham August 2012 University of Birmingham Research Archive e-theses repository This unpublished thesis/dissertation is copyright of the author and/or third parties. The intellectual property rights of the author or third parties in respect of this work are as defined by The Copyright Designs and Patents Act 1988 or as modified by any successor legislation. Any use made of information contained in this thesis/dissertation must be in accordance with that legislation and must be properly acknowledged. Further distribution or reproduction in any format is prohibited without the permission of the copyright holder. ABSTRACT Tumour angiogenesis is a vital process in the pathology of tumour development and metastasis. Targeting markers of tumour endothelium provide a means of targeted destruction of a tumours oxygen and nutrient supply via destruction of tumour vasculature, which in turn ultimately leads to beneficial consequences to patients. Although current anti -angiogenic and vascular targeting strategies help patients, more potently in combination with chemo therapy, there is still a need for more tumour endothelial marker discoveries as current treatments have cardiovascular and other side effects. For the first time, the analyses of in-vivo biotinylation of an embryonic system is performed to obtain putative vascular targets. Also for the first time, deep sequencing is applied to freshly isolated tumour and normal endothelial cells from lung, colon and bladder tissues for the identification of pan-vascular-targets. Integration of the proteomic, deep sequencing, public cDNA libraries and microarrays, delivers 5,892 putative vascular targets to the science community.
    [Show full text]
  • Shear Stress Modulates Gene Expression in Normal Human Dermal Fibroblasts
    University of Calgary PRISM: University of Calgary's Digital Repository Graduate Studies The Vault: Electronic Theses and Dissertations 2017 Shear Stress Modulates Gene Expression in Normal Human Dermal Fibroblasts Zabinyakov, Nikita Zabinyakov, N. (2017). Shear Stress Modulates Gene Expression in Normal Human Dermal Fibroblasts (Unpublished master's thesis). University of Calgary, Calgary, AB. doi:10.11575/PRISM/27775 http://hdl.handle.net/11023/3639 master thesis University of Calgary graduate students retain copyright ownership and moral rights for their thesis. You may use this material in any way that is permitted by the Copyright Act or through licensing that has been assigned to the document. For uses that are not allowable under copyright legislation or licensing, you are required to seek permission. Downloaded from PRISM: https://prism.ucalgary.ca UNIVERSITY OF CALGARY Shear Stress Modulates Gene Expression in Normal Human Dermal Fibroblasts by Nikita Zabinyakov A THESIS SUBMITTED TO THE FACULTY OF GRADUATE STUDIES IN PARTIAL FULFILMENT OF THE REQUIREMENTS FOR THE DEGREE OF MASTER OF SCIENCE GRADUATE PROGRAM IN BIOMEDICAL ENGINEERING CALGARY, ALBERTA JANUARY 2017 © Nikita Zabinyakov 2017 Abstract Applied mechanical forces, such as those resulting from fluid flow, trigger cells to change their functional behavior or phenotype. However, there is little known about how fluid flow affects fibroblasts. The hypothesis of this thesis is that dermal fibroblasts undergo significant changes of expression of differentiation genes after exposure to fluid flow (or shear stress). To test the hypothesis, human dermal fibroblasts were exposed to laminar steady fluid flow for 20 and 40 hours and RNA was collected for microarray analysis.
    [Show full text]
  • Download Special Issue
    BioMed Research International Novel Bioinformatics Approaches for Analysis of High-Throughput Biological Data Guest Editors: Julia Tzu-Ya Weng, Li-Ching Wu, Wen-Chi Chang, Tzu-Hao Chang, Tatsuya Akutsu, and Tzong-Yi Lee Novel Bioinformatics Approaches for Analysis of High-Throughput Biological Data BioMed Research International Novel Bioinformatics Approaches for Analysis of High-Throughput Biological Data Guest Editors: Julia Tzu-Ya Weng, Li-Ching Wu, Wen-Chi Chang, Tzu-Hao Chang, Tatsuya Akutsu, and Tzong-Yi Lee Copyright © 2014 Hindawi Publishing Corporation. All rights reserved. This is a special issue published in “BioMed Research International.” All articles are open access articles distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Contents Novel Bioinformatics Approaches for Analysis of High-Throughput Biological Data,JuliaTzu-YaWeng, Li-Ching Wu, Wen-Chi Chang, Tzu-Hao Chang, Tatsuya Akutsu, and Tzong-Yi Lee Volume2014,ArticleID814092,3pages Evolution of Network Biomarkers from Early to Late Stage Bladder Cancer Samples,Yung-HaoWong, Cheng-Wei Li, and Bor-Sen Chen Volume 2014, Article ID 159078, 23 pages MicroRNA Expression Profiling Altered by Variant Dosage of Radiation Exposure,Kuei-FangLee, Yi-Cheng Chen, Paul Wei-Che Hsu, Ingrid Y. Liu, and Lawrence Shih-Hsin Wu Volume2014,ArticleID456323,10pages EXIA2: Web Server of Accurate and Rapid Protein Catalytic Residue Prediction, Chih-Hao Lu, Chin-Sheng
    [Show full text]
  • Transcriptional Regulators Are Upregulated in the Substantia Nigra
    Journal of Emerging Investigators Transcriptional Regulators are Upregulated in the Substantia Nigra of Parkinson’s Disease Patients Marianne Cowherd1 and Inhan Lee2 1Community High School, Ann Arbor, MI 2miRcore, Ann Arbor, MI Summary neurological conditions is an established practice (3). Parkinson’s disease (PD) affects approximately 10 Significant gene expression dysregulation in the SN and million people worldwide with tremors, bradykinesia, in the striatum has been described, particularly decreased apathy, memory loss, and language issues. Though such expression in PD synapses. Protein degradation has symptoms are due to the loss of the substantia nigra (SN) been found to be upregulated (4). Mutations in SNCA brain region, the ultimate causes and complete pathology are unknown. To understand the global gene expression (5), LRRK2 (6), and GBA (6) have also been identified changes in SN, microarray expression data from the SN as familial markers of PD. SNCA encodes alpha- tissue of 9 controls and 16 PD patients were compared, synuclein, a protein found in presynaptic terminals that and significantly upregulated and downregulated may regulate vesicle presence and dopamine release. genes were identified. Among the upregulated genes, Eighteen SNCA mutations have been associated with a network of 33 interacting genes centered around the PD and, although the exact pathogenic mechanism is cAMP-response element binding protein (CREBBP) was not confirmed, mutated alpha-synuclein is the major found. The downstream effects of increased CREBBP- component of protein aggregates, called Lewy bodies, related transcription and the resulting protein levels that are often found in PD brains and may contribute may result in PD symptoms, making CREBBP a potential therapeutic target due to its central role in the interactive to cell death.
    [Show full text]
  • 393LN V 393P 344SQ V 393P Probe Set Entrez Gene
    393LN v 393P 344SQ v 393P Entrez fold fold probe set Gene Gene Symbol Gene cluster Gene Title p-value change p-value change chemokine (C-C motif) ligand 21b /// chemokine (C-C motif) ligand 21a /// chemokine (C-C motif) ligand 21c 1419426_s_at 18829 /// Ccl21b /// Ccl2 1 - up 393 LN only (leucine) 0.0047 9.199837 0.45212 6.847887 nuclear factor of activated T-cells, cytoplasmic, calcineurin- 1447085_s_at 18018 Nfatc1 1 - up 393 LN only dependent 1 0.009048 12.065 0.13718 4.81 RIKEN cDNA 1453647_at 78668 9530059J11Rik1 - up 393 LN only 9530059J11 gene 0.002208 5.482897 0.27642 3.45171 transient receptor potential cation channel, subfamily 1457164_at 277328 Trpa1 1 - up 393 LN only A, member 1 0.000111 9.180344 0.01771 3.048114 regulating synaptic membrane 1422809_at 116838 Rims2 1 - up 393 LN only exocytosis 2 0.001891 8.560424 0.13159 2.980501 glial cell line derived neurotrophic factor family receptor alpha 1433716_x_at 14586 Gfra2 1 - up 393 LN only 2 0.006868 30.88736 0.01066 2.811211 1446936_at --- --- 1 - up 393 LN only --- 0.007695 6.373955 0.11733 2.480287 zinc finger protein 1438742_at 320683 Zfp629 1 - up 393 LN only 629 0.002644 5.231855 0.38124 2.377016 phospholipase A2, 1426019_at 18786 Plaa 1 - up 393 LN only activating protein 0.008657 6.2364 0.12336 2.262117 1445314_at 14009 Etv1 1 - up 393 LN only ets variant gene 1 0.007224 3.643646 0.36434 2.01989 ciliary rootlet coiled- 1427338_at 230872 Crocc 1 - up 393 LN only coil, rootletin 0.002482 7.783242 0.49977 1.794171 expressed sequence 1436585_at 99463 BB182297 1 - up 393
    [Show full text]
  • UC Berkeley UC Berkeley Previously Published Works
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by eScholarship - University of California UC Berkeley UC Berkeley Previously Published Works Title THAP proteins target specific DNA sites through bipartite recognition of adjacent major and minor grooves. Permalink https://escholarship.org/uc/item/4hd07091 Journal Nature Structural and Molecular Biology, 17(1) Authors Sabogal, Alex Lyubimov, Artem Corn, Jacob et al. Publication Date 2010 DOI 10.1038/nsmb.1742 Peer reviewed eScholarship.org Powered by the California Digital Library University of California HHS Public Access Author manuscript Author Manuscript Author ManuscriptNat Struct Author Manuscript Mol Biol. Author Author Manuscript manuscript; available in PMC 2010 September 06. Published in final edited form as: Nat Struct Mol Biol. 2010 January ; 17(1): 117–123. doi:10.1038/nsmb.1742. THAP proteins target specific DNA sites through bipartite recognition of adjacent major and minor grooves Alex Sabogal1,*, Artem Y. Lyubimov1,2,*, Jacob E. Corn1, James M. Berger1,2,†, and Donald C. Rio1,2,3,† 1Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA 2California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA 3Center for Integrative Genomics, University of California, Berkeley, Berkeley, CA 94720, USA Abstract THAP-family C2CH zinc-coordinating DNA-binding proteins function in diverse eukaryotic cellular processes, such as transposition, transcriptional repression, stem-cell pluripotency, angiogenesis and neurological function. To determine the molecular basis for sequence-specific DNA recognition by THAP proteins, we solved the crystal structure of the Drosophila melanogaster P element transposase THAP domain (DmTHAP) complexed with a natural 10-base pair site.
    [Show full text]
  • Signatures of Tspan8 Variants Associated with Human
    bioRxiv preprint doi: https://doi.org/10.1101/2020.11.17.386839; this version posted November 19, 2020. 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. SIGNATURES OF TSPAN8 VARIANTS ASSOCIATED WITH HUMAN METABOLIC REGULATION AND DISEASES 1,2,3,§ 4,5 6,7,8 3,9 Tisham De ,​ Angela Goncalves ,​ Doug Speed ,​ Phillipe Froguel ,​ NFBC consortium, Daniel ​ ​ ​ ​ 4 10, 11,12,13,14 1,2,15 Gaffney ,​ Michael R. Johnson *,​ Maarjo-Riitta Jarvelin *,​ Lachlan JM Coin *​ ​ ​ ​ ​ 1. Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, UK 2. Department of Genomics of Common Diseases, Imperial College London, UK 3. Department of Metabolism, Imperial College London, London, UK. 4. Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK 5. German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany 6. Bioinformatics Research Centre (BiRC), Aarhus University, Denmark. 7. Aarhus Institute of Advanced Studies (AIAS), Aarhus University, Denmark. 8. Quantitative Genetics and Genomics (QGG), Aarhus University, Denmark. 9. Inserm UMR1283, CNRS UMR8199, European Genomic Institute for Diabetes (EGID), Université de Lille, Institut Pasteur de Lille, Lille University Hospital, Lille, France 10. Department of Brain Sciences, Imperial College London, UK 11. Centre for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland 12. Unit of Primary Health Care and Medical Research Center, Oulu University Hospital, Oulu, Finland 13. Department of Epidemiology and Biostatistics, Medical Research Council–Public Health England Centre for Environment and Health, Imperial College London, London, UK 14.
    [Show full text]
  • Downloaded from Ensembl
    UCSF UC San Francisco Electronic Theses and Dissertations Title Detecting genetic similarity between complex human traits by exploring their common molecular mechanism Permalink https://escholarship.org/uc/item/1k40s443 Author Gu, Jialiang Publication Date 2019 Peer reviewed|Thesis/dissertation eScholarship.org Powered by the California Digital Library University of California by Submitted in partial satisfaction of the requirements for degree of in in the GRADUATE DIVISION of the UNIVERSITY OF CALIFORNIA, SAN FRANCISCO AND UNIVERSITY OF CALIFORNIA, BERKELEY Approved: ______________________________________________________________________________ Chair ______________________________________________________________________________ ______________________________________________________________________________ ______________________________________________________________________________ ______________________________________________________________________________ Committee Members ii Acknowledgement This project would not have been possible without Prof. Dr. Hao Li, Dr. Jiashun Zheng and Dr. Chris Fuller at the University of California, San Francisco (UCSF) and Caribou Bioscience. The Li lab grew into a multi-facet research group consist of both experimentalists and computational biologists covering three research areas including cellular/molecular mechanism of ageing, genetic determinants of complex human traits and structure, function, evolution of gene regulatory network. Labs like these are the pillar of global success and reputation
    [Show full text]
  • Knockdown of Hnrnpa0, a Del(5Q) Gene, Alters Myeloid Cell Fate In
    Myelodysplastic Syndromes SUPPLEMENTARY APPENDIX Knockdown of Hnrnpa0 , a del(5q) gene, alters myeloid cell fate in murine cells through regulation of AU-rich transcripts David J. Young, 1 Angela Stoddart, 2 Joy Nakitandwe, 3 Shann-Ching Chen, 3 Zhijian Qian, 4 James R. Downing, 3 and Michelle M. Le Beau 2 1Department of Pediatrics, Division of Oncology, Johns Hopkins University, Baltimora, MD; 2Department of Medicine and the Compre - hensive Cancer Center, University of Chicago, IL; 3St. Jude Children's Research Hospital, Memphis, Tennessee; and 4University of Illi - nois Cancer Center, Chicago, IL, USA DJY and AS equally contributed to this work. ©2014 Ferrata Storti Foundation. This is an open-access paper. doi:10.3324/haematol.2013.098657 Manuscript received on September 25, 2013. Manuscript accepted on February 13, 2014. Correspondence: [email protected] Supplementary Materials for D. Young et al. Purification of hematopoietic populations from mice. Cells from the spleens, thymi, and bone marrow of C57BL/6J mice were harvested as appropriate for each population. For primitive populations including Lin–Sca-1+Kit+ (LSK), common lymphoid (CLP) and myeloid (CMP) progenitors, and granulocyte- monocyte progenitors (GMP), the cells were depleted of mature cells using the Mouse Hematopoietic Progenitor Cell Enrichment Kit (StemCell Technologies). The cells were stained for appropriate lineage markers, as described in Supplementary Figure S1, and sorted using a FACSAria fluorescence activated cell sorter (BD Biosciences). Real-time RT-PCR analysis Total RNA was purified from cells using Stat-60 (Tel-Test), according to the manufacturer’s protocols. First-strand cDNA was synthesized using SuperScript III SuperMix for qRT-PCR (Invitrogen) containing both random hexamers and oligo(dT)20 for priming.
    [Show full text]
  • Clinical Efficacy and Immune Regulation with Peanut Oral
    Clinical efficacy and immune regulation with peanut oral immunotherapy Stacie M. Jones, MD,a Laurent Pons, PhD,b Joseph L. Roberts, MD, PhD,b Amy M. Scurlock, MD,a Tamara T. Perry, MD,a Mike Kulis, PhD,b Wayne G. Shreffler, MD, PhD,c Pamela Steele, CPNP,b Karen A. Henry, RN,a Margaret Adair, MD,b James M. Francis, PhD,d Stephen Durham, MD,d Brian P. Vickery, MD,b Xiaoping Zhong, MD, PhD,b and A. Wesley Burks, MDb Little Rock, Ark, Durham, NC, New York, NY, and London, United Kingdom Background: Oral immunotherapy (OIT) has been thought to noted during OIT resolved spontaneously or with induce clinical desensitization to allergenic foods, but trials antihistamines. By 6 months, titrated skin prick tests and coupling the clinical response and immunologic effects of peanut activation of basophils significantly declined. Peanut-specific OIT have not been reported. IgE decreased by 12 to 18 months, whereas IgG4 increased Objective: The study objective was to investigate the clinical significantly. Serum factors inhibited IgE–peanut complex efficacy and immunologic changes associated with OIT. formation in an IgE-facilitated allergen binding assay. Secretion Methods: Children with peanut allergy underwent an OIT of IL-10, IL-5, IFN-g, and TNF-a from PBMCs increased over protocol including initial day escalation, buildup, and a period of 6 to 12 months. Peanut-specific forkhead box protein maintenance phases, and then oral food challenge. Clinical 3 T cells increased until 12 months and decreased thereafter. In response and immunologic changes were evaluated. addition, T-cell microarrays showed downregulation of genes in Results: Of 29 subjects who completed the protocol, 27 ingested apoptotic pathways.
    [Show full text]
  • 1 the Origin of Genome Instability in Cancer
    The Origin of Genome Instability in Cancer: Role of the Fragile Site Gene Product FHIT Dissertation Presented in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of The Ohio State University By Joshua Charles Saldivar, M.S. Biomedical Sciences Graduate Program The Ohio State University 2013 Dissertation Committee: Kay Huebner, PhD, Advisor Carlo Croce, MD Joanna Groden, PhD Denis Guttridge, PhD 1 Copyright by Joshua Charles Saldivar 2013 2 ABSTRACT The transformation of normal cells to cancer cells involves multiple steps mediated by the acquisition of mutations, selection and clonal expansion of cells with favorable mutations. Most cancers exhibit remarkable genomic instability, defined as an elevated rate of genetic mutation at the single nucleotide and chromosome levels. Genomic instability is a facilitating hallmark of cancer in that it raises the probability of generating cancer-promoting mutations. Multiple factors contribute to the genome instability phenotypes seen in cancer, but the molecular processes initiating instability in sporadic cancer are unknown. In dysplastic cells, genomic alterations are first seen at chromosome fragile sites. These fragile sites are exquisitely sensitive to agents that stress DNA replication forks, and thus, it is thought that replicative stress is a major source of genome instability in cancer. A frequent and very early genetic alteration in precancerous cells is deletion within fragile site FRA3B, which overlaps exons of the large FHIT gene, resulting in loss of FHIT protein expression. Here it is shown that loss of FHIT expression triggers endogenous replication stress hindering replication fork progression and inducing fork stalling and collapse.
    [Show full text]