DOCSLIB.ORG

Mouse Phldb2 Knockout Project (CRISPR/Cas9)

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Mouse Phldb2 Knockout Project (CRISPR/Cas9) https://www.alphaknockout.com Mouse Phldb2 Knockout Project (CRISPR/Cas9) Objective: To create a Phldb2 knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering. Strategy summary: The Phldb2 gene (NCBI Reference Sequence: NM_001252442 ; Ensembl: ENSMUSG00000033149 ) is located on Mouse chromosome 16. 19 exons are identified, with the ATG start codon in exon 2 and the TAG stop codon in exon 19 (Transcript: ENSMUST00000076333). Exon 2 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: Mice homozygous for a conditional allele activated in neurons exhibit impaired LTP. Exon 2 starts from the coding region. Exon 2 covers 33.87% of the coding region. The size of effective KO region: ~1337 bp. The KO region does not have any other known gene. Page 1 of 9 https://www.alphaknockout.com Overview of the Targeting Strategy Wildtype allele 5' gRNA region gRNA region 3' 1 2 19 Legends Exon of mouse Phldb2 Knockout region Page 2 of 9 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. Tandem repeats are found in the dot plot matrix. The gRNA site is selected outside of these tandem repeats. Overview of the Dot Plot (down) Window size: 15 bp Forward Reverse Complement Sequence 12 Note: The 2000 bp section downstream 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. Page 3 of 9 https://www.alphaknockout.com Overview of the GC Content Distribution (up) Window size: 300 bp Sequence 12 Summary: Full Length(2000bp) | A(30.65% 613) | C(17.55% 351) | T(33.35% 667) | G(18.45% 369) Note: The 2000 bp section upstream of Exon 2 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. Overview of the GC Content Distribution (down) Window size: 300 bp Sequence 12 Summary: Full Length(2000bp) | A(29.2% 584) | C(20.25% 405) | T(32.7% 654) | G(17.85% 357) Note: The 2000 bp section downstream of Exon 2 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 4 of 9 https://www.alphaknockout.com BLAT Search Results (up) QUERY SCORE START END QSIZE IDENTITY CHROM STRAND START END SPAN ----------------------------------------------------------------------------------------------- browser details YourSeq 2000 1 2000 2000 100.0% chr16 - 45826082 45828081 2000 browser details YourSeq 55 76 244 2000 92.2% chr3 + 60249907 60250710 804 browser details YourSeq 54 93 152 2000 96.7% chr17 - 85969726 85969791 66 browser details YourSeq 50 73 152 2000 98.1% chr11 - 68488759 68488876 118 browser details YourSeq 47 86 165 2000 87.5% chr2 - 43007845 43007922 78 browser details YourSeq 46 105 156 2000 98.0% chr1 - 180181024 180181087 64 browser details YourSeq 40 73 124 2000 97.7% chr3 + 30190123 30190194 72 browser details YourSeq 37 76 121 2000 93.4% chr12 + 7422777 7422834 58 browser details YourSeq 34 74 119 2000 81.1% chr18 + 43121623 43121664 42 browser details YourSeq 32 94 131 2000 94.8% chr4 + 100693959 100694008 50 browser details YourSeq 32 73 105 2000 100.0% chr13 + 88752862 88752896 35 browser details YourSeq 32 96 152 2000 79.0% chr1 + 99725138 99725201 64 browser details YourSeq 31 78 115 2000 94.5% chr14 + 83006092 83006137 46 browser details YourSeq 31 78 156 2000 97.0% chr1 + 167619074 167619290 217 browser details YourSeq 30 92 124 2000 87.1% chr12 - 7792326 7792356 31 browser details YourSeq 30 78 114 2000 85.3% chr1 - 109299423 109299457 35 browser details YourSeq 30 78 160 2000 59.4% chr7 + 80853790 80853822 33 browser details YourSeq 30 76 156 2000 59.4% chr16 + 55840816 55840848 33 browser details YourSeq 29 76 106 2000 96.8% chr2 - 136221670 136221700 31 browser details YourSeq 29 74 108 2000 91.5% chr5 + 65562512 65562546 35 Note: The 2000 bp section upstream of Exon 2 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 2000 1 2000 2000 100.0% chr16 - 45822759 45824758 2000 browser details YourSeq 27 1140 1169 2000 96.6% chr14 + 123205537 123205571 35 browser details YourSeq 26 668 693 2000 100.0% chr7 + 14343965 14343990 26 browser details YourSeq 23 367 397 2000 87.1% chr7 - 136094616 136094646 31 browser details YourSeq 21 1173 1193 2000 100.0% chr9 + 40940401 40940421 21 Note: The 2000 bp section downstream of Exon 2 is BLAT searched against the genome. No significant similarity is found. Page 5 of 9 https://www.alphaknockout.com Gene and protein information: Phldb2 pleckstrin homology like domain, family B, member 2 [ Mus musculus (house mouse) ] Gene ID: 208177, updated on 12-Aug-2019 Gene summary Official Symbol Phldb2 provided by MGI Official Full Name pleckstrin homology like domain, family B, member 2 provided by MGI Primary source MGI:MGI:2444981 See related Ensembl:ENSMUSG00000033149 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 LL5b; LL5beta; AV253284; C820004H04Rik Expression Broad expression in bladder adult (RPKM 19.0), limb E14.5 (RPKM 13.1) and 20 other tissues See more Orthologs human all Genomic context Location: 16; 16 B5 See Phldb2 in Genome Data Viewer Exon count: 25 Annotation release Status Assembly Chr Location 108 current GRCm38.p6 (GCF_000001635.26) 16 NC_000082.6 (45746230..45953598, complement) Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 16 NC_000082.5 (45746346..45844491, complement) Chromosome 16 - NC_000082.6 Page 6 of 9 https://www.alphaknockout.com Transcript information: This gene has 11 transcripts Gene: Phldb2 ENSMUSG00000033149 Description pleckstrin homology like domain, family B, member 2 [Source:MGI Symbol;Acc:MGI:2444981] Gene Synonyms C820004H04Rik, LL5b, LL5beta Location Chromosome 16: 45,746,243-45,953,598 reverse strand. GRCm38:CM001009.2 About this gene This gene has 11 transcripts (splice variants), 317 orthologues, 6 paralogues and is a member of 1 Ensembl protein family. Transcripts Name Transcript ID bp Protein Translation ID Biotype CCDS UniProt Flags Phldb2-201 ENSMUST00000036355.12 5483 1249aa ENSMUSP00000046496.6 Protein coding CCDS28202 Q8K1N2 TSL:1 GENCODE basic APPRIS P3 Phldb2-202 ENSMUST00000076333.11 5347 1302aa ENSMUSP00000075672.5 Protein coding CCDS57031 Q8K1N2 TSL:1 GENCODE basic APPRIS ALT2 Phldb2-207 ENSMUST00000134802.7 3612 1131aa ENSMUSP00000123284.1 Protein coding - D3Z069 CDS 3' incomplete TSL:1 Phldb2-205 ENSMUST00000131003.7 2328 565aa ENSMUSP00000119718.1 Protein coding - F6QU68 CDS 5' incomplete TSL:1 Phldb2-209 ENSMUST00000136405.1 595 133aa ENSMUSP00000121800.1 Protein coding - D3Z231 CDS 3' incomplete TSL:3 Phldb2-206 ENSMUST00000133111.2 614 No protein - Retained intron - - TSL:5 Phldb2-204 ENSMUST00000128365.2 831 No protein - lncRNA - - TSL:5 Phldb2-211 ENSMUST00000151300.1 664 No protein - lncRNA - - TSL:3 Phldb2-208 ENSMUST00000136317.1 497 No protein - lncRNA - - TSL:2 Phldb2-210 ENSMUST00000142697.1 467 No protein - lncRNA - - TSL:5 Phldb2-203 ENSMUST00000125433.1 343 No protein - lncRNA - - TSL:3 Page 7 of 9 https://www.alphaknockout.com 227.36 kb Forward strand 45.75Mb 45.80Mb 45.85Mb 45.90Mb 45.95Mb Genes Gm15591-201 >lncRNA Gm15640-201 >lncRNA (Comprehensive set... Gm15638-203 >lncRNA Gm15638-201 >lncRNA Gm15638-202 >lncRNA Contigs < AC166572.1 AC164979.2 > Genes (Comprehensive set... < Abhd10-201protein coding < Phldb2-206retained intron < Phldb2-209protein coding < Abhd10-202nonsense mediated decay < Phldb2-203lncRNA < Phldb2-204lncRNA < Plcxd2-201protein coding < Abhd10-203lncRNA< Phldb2-211lncRNA < Phldb2-208lncRNA < Abhd10-204lncRNA < Phldb2-210lncRNA < Abhd10-205lncRNA < Phldb2-201protein coding < Phldb2-202protein coding < Phldb2-205protein coding < Phldb2-207protein coding Regulatory Build 45.75Mb 45.80Mb 45.85Mb 45.90Mb 45.95Mb Reverse strand 227.36 kb Regulation Legend CTCF Enhancer Open Chromatin Promoter Promoter Flank Transcription Factor Binding Site Gene Legend Protein Coding Ensembl protein coding merged Ensembl/Havana Non-Protein Coding RNA gene processed transcript Page 8 of 9 https://www.alphaknockout.com Transcript: ENSMUST00000076333 < Phldb2-202protein coding Reverse strand 97.84 kb ENSMUSP00000075... MobiDB lite Low complexity (Seg) Coiled-coils (Ncoils) Superfamily SSF50729 SMART Pleckstrin homology domain Pfam Pleckstrin homology domain PROSITE profiles Pleckstrin homology domain PANTHER PTHR12156:SF21 PTHR12156 Gene3D PH-like domain superfamily CDD PHLDB1/2/3, PH domain All sequence SNPs/i... Sequence variants (dbSNP and all other sources) Variant Legend missense variant synonymous variant Scale bar 0 200 400 600 800 1000 1302 We wish to acknowledge the following valuable scientific information resources: Ensembl, MGI, NCBI, UCSC. Page 9 of 9.
Load more

Recommended publications
  • CLASP2 Antibody Product Type
    PRODUCT INFORMATION Product name： CLASP2 antibody Product type： Primary antibodies Description： Rabbit polyclonal to CLASP2 Immunogen：3 synthetic peptides (human) conjugated to KLH Reacts with：Hu, Ms Tested applications：ELISA, WB and IF GENE INFORMATION Gene Symbol： CLASP2 Gene Name：cytoplasmic linker associated protein 2 Ensembl ID：ENSG00000163539 Entrez GeneID：23122 GenBank Accession number：AB014527 Swiss-Prot：O75122 Molecular weight of CLASP2： 165.9 & 108.6kDa Function：Microtubule plus-end tracking protein that promotes the stabilization of dynamic microtubules. Involved in the nucleation of noncentrosomal microtubules originating from the trans-Golgi network (TGN). Required for the polarization of the cytoplasmic microtubule arrays in migrating cells towards the leading edge of the cell. May act at the cell cortex to enhance the frequency of rescue of depolymerizing microtubules by attaching their plus- ends to cortical platforms composed of ERC1 and PHLDB2. This cortical microtubule stabilizing activity is regulated at least in part by phosphatidylinositol 3-kinase signaling. Also performs a similar stabilizing function at the kinetochore which is essential for the bipolar alignment of chromosomes on the mitotic spindle. Acts as a mediator of ERBB2- dependent stabilization of microtubules at the cell cortex. Expected subcellular localization：Cytoplasm › cytoskeleton. Cytoplasm › cytoskeleton › microtubule organizing center › centrosome. Chromosome › centromere › kinetochore. Cytoplasm › cytoskeleton › spindle. Golgi apparatus. Golgi apparatus › trans-Golgi network. Cell membrane. Cell projection › ruffle membrane. Note: Localizes to microtubule plus ends. Localizes to centrosomes, kinetochores and the mitotic spindle from prometaphase. Subsequently localizes to the spindle midzone from anaphase and to the midbody from telophase. In migrating cells localizes to the plus ends of microtubules within the cell body and to the entire microtubule lattice within the lamella.
    [Show full text]
  • Long-Range Chromosome Interactions Mediated by Cohesin Shape Circadian Gene Expression
    RESEARCH ARTICLE Long-Range Chromosome Interactions Mediated by Cohesin Shape Circadian Gene Expression Yichi Xu1,2, Weimin Guo1, Ping Li3, Yan Zhang3, Meng Zhao1,4, Zenghua Fan1,2, Zhihu Zhao3, Jun Yan1,4* 1 CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China, 2 University of Chinese Academy of Sciences, Shanghai, China, 3 Beijing Institute of Biotechnology, Beijing, China, 4 Institute of Neuroscience, State Key Laboratory a11111 of Neuroscience, CAS Center for Excellence in Brain Science, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China * [email protected] Abstract OPEN ACCESS Mammalian circadian rhythm is established by the negative feedback loops consisting of a Citation: Xu Y, Guo W, Li P, Zhang Y, Zhao M, Fan Z, et al. (2016) Long-Range Chromosome Interactions set of clock genes, which lead to the circadian expression of thousands of downstream Mediated by Cohesin Shape Circadian Gene genes in vivo. As genome-wide transcription is organized under the high-order chromosome Expression. PLoS Genet 12(5): e1005992. structure, it is largely uncharted how circadian gene expression is influenced by chromo- doi:10.1371/journal.pgen.1005992 some architecture. We focus on the function of chromatin structure proteins cohesin as well — Editor: Achim Kramer, Charité Universitätsmedizin as CTCF (CCCTC-binding factor) in circadian rhythm. Using circular chromosome confor- Berlin, GERMANY mation capture sequencing, we systematically examined the interacting loci of a Bmal1- Received: October 10, 2015 bound super-enhancer upstream of a clock gene Nr1d1 in mouse liver. These interactions Accepted: March 27, 2016 are largely stable in the circadian cycle and cohesin binding sites are enriched in the interac- Published: May 2, 2016 tome.
    [Show full text]
  • Genomic and Transcriptome Analysis Revealing an Oncogenic Functional Module in Meningiomas
    Neurosurg Focus 35 (6):E3, 2013 ©AANS, 2013 Genomic and transcriptome analysis revealing an oncogenic functional module in meningiomas XIAO CHANG, PH.D.,1 LINGLING SHI, PH.D.,2 FAN GAO, PH.D.,1 JONATHAN RUssIN, M.D.,3 LIYUN ZENG, PH.D.,1 SHUHAN HE, B.S.,3 THOMAS C. CHEN, M.D.,3 STEVEN L. GIANNOTTA, M.D.,3 DANIEL J. WEISENBERGER, PH.D.,4 GAbrIEL ZADA, M.D.,3 KAI WANG, PH.D.,1,5,6 AND WIllIAM J. MAck, M.D.1,3 1Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, California; 2GHM Institute of CNS Regeneration, Jinan University, Guangzhou, China; 3Department of Neurosurgery, Keck School of Medicine, University of Southern California, Los Angeles, California; 4USC Epigenome Center, Keck School of Medicine, University of Southern California, Los Angeles, California; 5Department of Psychiatry, Keck School of Medicine, University of Southern California, Los Angeles, California; and 6Division of Bioinformatics, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California Object. Meningiomas are among the most common primary adult brain tumors. Although typically benign, roughly 2%–5% display malignant pathological features. The key molecular pathways involved in malignant trans- formation remain to be determined. Methods. Illumina expression microarrays were used to assess gene expression levels, and Illumina single- nucleotide polymorphism arrays were used to identify copy number variants in benign, atypical, and malignant me- ningiomas (19 tumors, including 4 malignant ones). The authors also reanalyzed 2 expression data sets generated on Affymetrix microarrays (n = 68, including 6 malignant ones; n = 56, including 3 malignant ones).
    [Show full text]
  • Caracterización De Complejos CDK-Ciclina Atípicos Humanos Eva Quandt Herrera
    Caracterización de complejos CDK-Ciclina atípicos humanos Eva Quandt Herrera ADVERTIMENT. La consulta d’aquesta tesi queda condicionada a l’acceptació de les següents condicions d'ús: La difusió d’aquesta tesi per mitjà del servei TDX (www.tesisenxarxa.net) ha estat autoritzada pels titulars dels drets de propietat intel·lectual únicament per a usos privats emmarcats en activitats d’investigació i docència. No s’autoritza la seva reproducció amb finalitats de lucre ni la seva difusió i posada a disposició des d’un lloc aliè al servei TDX. No s’autoritza la presentació del seu contingut en una finestra o marc aliè a TDX (framing). Aquesta reserva de drets afecta tant al resum de presentació de la tesi com als seus continguts. En la utilització o cita de parts de la tesi és obligat indicar el nom de la persona autora. ADVERTENCIA. La consulta de esta tesis queda condicionada a la aceptación de las siguientes condiciones de uso: La difusión de esta tesis por medio del servicio TDR (www.tesisenred.net) ha sido autorizada por los titulares de los derechos de propiedad intelectual únicamente para usos privados enmarcados en actividades de investigación y docencia. No se autoriza su reproducción con finalidades de lucro ni su difusión y puesta a disposición desde un sitio ajeno al servicio TDR. No se autoriza la presentación de su contenido en una ventana o marco ajeno a TDR (framing). Esta reserva de derechos afecta tanto al resumen de presentación de la tesis como a sus contenidos. En la utilización o cita de partes de la tesis es obligado indicar el nombre de la persona autora.
    [Show full text]
  • ID AKI Vs Control Fold Change P Value Symbol Entrez Gene Name *In
    ID AKI vs control P value Symbol Entrez Gene Name *In case of multiple probesets per gene, one with the highest fold change was selected. Fold Change 208083_s_at 7.88 0.000932 ITGB6 integrin, beta 6 202376_at 6.12 0.000518 SERPINA3 serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 3 1553575_at 5.62 0.0033 MT-ND6 NADH dehydrogenase, subunit 6 (complex I) 212768_s_at 5.50 0.000896 OLFM4 olfactomedin 4 206157_at 5.26 0.00177 PTX3 pentraxin 3, long 212531_at 4.26 0.00405 LCN2 lipocalin 2 215646_s_at 4.13 0.00408 VCAN versican 202018_s_at 4.12 0.0318 LTF lactotransferrin 203021_at 4.05 0.0129 SLPI secretory leukocyte peptidase inhibitor 222486_s_at 4.03 0.000329 ADAMTS1 ADAM metallopeptidase with thrombospondin type 1 motif, 1 1552439_s_at 3.82 0.000714 MEGF11 multiple EGF-like-domains 11 210602_s_at 3.74 0.000408 CDH6 cadherin 6, type 2, K-cadherin (fetal kidney) 229947_at 3.62 0.00843 PI15 peptidase inhibitor 15 204006_s_at 3.39 0.00241 FCGR3A Fc fragment of IgG, low affinity IIIa, receptor (CD16a) 202238_s_at 3.29 0.00492 NNMT nicotinamide N-methyltransferase 202917_s_at 3.20 0.00369 S100A8 S100 calcium binding protein A8 215223_s_at 3.17 0.000516 SOD2 superoxide dismutase 2, mitochondrial 204627_s_at 3.04 0.00619 ITGB3 integrin, beta 3 (platelet glycoprotein IIIa, antigen CD61) 223217_s_at 2.99 0.00397 NFKBIZ nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, zeta 231067_s_at 2.97 0.00681 AKAP12 A kinase (PRKA) anchor protein 12 224917_at 2.94 0.00256 VMP1/ mir-21likely ortholog
    [Show full text]
  • Human-Specific Tandem Repeat Expansion and Differential Gene Expression During Primate Evolution
    Human-specific tandem repeat expansion and differential gene expression during primate evolution Arvis Sulovaria, Ruiyang Lia, Peter A. Audanoa, David Porubskya, Mitchell R. Vollgera, Glennis A. Logsdona, Human Genome Structural Variation Consortium1, Wesley C. Warrenb, Alex A. Pollenc, Mark J. P. Chaissona,d, and Evan E. Eichlera,e,2 aDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195; bBond Life Sciences Center, University of Missouri, Columbia, MO 65201; cDepartment of Neurology, University of California, San Francisco, CA 94143; dQuantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089; and eHoward Hughes Medical Institute, University of Washington, Seattle, WA 98195 Edited by Stephen T. Warren, Emory University School of Medicine, Atlanta, GA, and approved October 1, 2019 (received for review July 17, 2019) Short tandem repeats (STRs) and variable number tandem repeats Despite their established importance in population genetics (VNTRs) are important sources of natural and disease-causing and disease association, tandem repeats, particularly VNTRs, variation, yet they have been problematic to resolve in reference are among the least characterized forms of genetic variation in genomes and genotype with short-read technology. We created a the human genome (13, 14). Their repetitive nature and some- framework to model the evolution and instability of STRs and VNTRs times extreme GC content make them particularly challenging to in apes. We phased and assembled 3 ape genomes (chimpanzee, sequence and assemble with standard whole-genome shotgun gorilla, and orangutan) using long-read and 10x Genomics linked- sequencing assembly strategies, including next generation se- read sequence data for 21,442 human tandem repeats discovered in quencing approaches that depend on bridge amplification (15).
    [Show full text]
  • Chamber-Enriched Gene Expression Profiles in Failing Human Hearts with Reduced Ejection Fraction
    www.nature.com/scientificreports OPEN Chamber‑enriched gene expression profles in failing human hearts with reduced ejection fraction Xin Luo1, Jun Yin1, Denise Dwyer2, Tracy Yamawaki1, Hong Zhou1, Hongfei Ge3, Chun‑Ya Han2, Artem Shkumatov4, Karen Snyder5, Brandon Ason3, Chi‑Ming Li1, Oliver Homann1 & Marina Stolina2* Heart failure with reduced ejection fraction (HFrEF) constitutes 50% of HF hospitalizations and is characterized by high rates of mortality. To explore the underlying mechanisms of HFrEF etiology and progression, we studied the molecular and cellular diferences in four chambers of non‑failing (NF, n = 10) and HFrEF (n = 12) human hearts. We identifed 333 genes enriched within NF heart subregions and often associated with cardiovascular disease GWAS variants. Expression analysis of HFrEF tissues revealed extensive disease‑associated transcriptional and signaling alterations in left atrium (LA) and left ventricle (LV). Common left heart HFrEF pathologies included mitochondrial dysfunction, cardiac hypertrophy and fbrosis. Oxidative stress and cardiac necrosis pathways were prominent within LV, whereas TGF‑beta signaling was evident within LA. Cell type composition was estimated by deconvolution and revealed that HFrEF samples had smaller percentage of cardiomyocytes within the left heart, higher representation of fbroblasts within LA and perivascular cells within the left heart relative to NF samples. We identifed essential modules associated with HFrEF pathology and linked transcriptome discoveries with human genetics fndings. This study contributes to a growing body of knowledge describing chamber‑specifc transcriptomics and revealed genes and pathways that are associated with heart failure pathophysiology, which may aid in therapeutic target discovery. By physiological function, the human heart is a muscular pump that circulates blood, perfusing tissues through- out the body.
    [Show full text]
  • Study of Z-Disc-Associated Signaling Networks in Skeletal Muscle Cells by Functional and Global Phosphoproteomics
    PHDTHESIS Study of Z-disc-associated Signaling Networks in Skeletal Muscle Cells by Functional and Global Phosphoproteomics Inaugural-Dissertation zur Erlangung der Doktorwürde der Fakultät für Biologie der Albert-Ludwigs-Universität Freiburg im Breisgau vorgelegt von Lena Reimann geboren in Bielefeld Freiburg im Breisgau 01.08.2016 Angefertigt am Institut für Biologie II AG Biochemie und Funktionelle Proteomforschung zellulärer Systeme unter der Leitung von Prof. Dr. Bettina Warscheid Dekan der Fakultät für Biologie: Prof. Dr. Wolfgang Driever Promotionsvorsitzender: Prof. Dr. Stefan Rotter Betreuer der Arbeit: Prof. Dr. Bettina Warscheid Referent: Prof. Dr. Bettina Warscheid Koreferent:Prof. Dr. Jörn Dengjel Drittprüfer: Prof. Dr. Gerald Radziwill Datum der mündlichen Prüfung:21.10.2016 ART IS I, science is we. - Claude Bernard Zusammenfassung Als essentielle, strukturgebende Komponente des Sarkomers spielt die Z-Scheibe eine maßge- liche Rolle für die Funktionalität der quergestreiften Muskulatur. Die stetige Identifizierung von neuen Z-Scheiben-lokalisierten Proteinen, sowie deren Relevanz in muskulären Krankheits- bildern, hat die Z-Scheibe zunehmend in den Fokus der aktuellen Forschung gerückt. Neben ihrer strukturgebenden Funktion zeigen neuere Studien, dass die Z-Scheibe ein Hotspot für Signalprozesse in Muskelzellen ist. Bisher gibt es jedoch keine globalen Untersuchungen zur Aufklärung der komplexen Signalwege assoziiert mit dieser Struktur. Um Z-Scheiben-assoziierte Signalprozesse näher zu charakterisieren, wurde im ersten Teil dieser Arbeit eine großangelegte Phosphoproteomstudie mit ausdifferenzierten, kon- trahierenden C2C12 Myotuben durchgeführt. Zu diesem Zweck wurden die tryptisch ver- dauten Proteine mittels SCX-Chromatographie fraktioniert. Die anschließende Phosphopep- tidanreicherung erfolgte mit Titandioxid, gefolgt von einer hochauflösenden massenspek- trometrischen Analyse. Insgesamt wurden 11.369 Phosphorylierungsstellen, darunter 586 in sarkomerischen Proteinen gefunden.
    [Show full text]
  • Downloaded, Each with Over 20 Samples for AD-Specific Pathways, Biological Processes, and Driver Each Specific Brain Region in Each Condition
    Xiang et al. BMC Medical Genomics 2018, 11(Suppl 6):115 https://doi.org/10.1186/s12920-018-0431-1 RESEARCH Open Access Condition-specific gene co-expression network mining identifies key pathways and regulators in the brain tissue of Alzheimer’s disease patients Shunian Xiang1,2, Zhi Huang4, Wang Tianfu1, Zhi Han3, Christina Y. Yu3,5, Dong Ni1*, Kun Huang3* and Jie Zhang2* From 29th International Conference on Genome Informatics Yunnan, China. 3-5 December 2018 Abstract Background: Gene co-expression network (GCN) mining is a systematic approach to efficiently identify novel disease pathways, predict novel gene functions and search for potential disease biomarkers. However, few studies have systematically identified GCNs in multiple brain transcriptomic data of Alzheimer’s disease (AD) patients and looked for their specific functions. Methods: In this study, we first mined GCN modules from AD and normal brain samples in multiple datasets respectively; then identified gene modules that are specific to AD or normal samples; lastly, condition-specific modules with similar functional enrichments were merged and enriched differentially expressed upstream transcription factors were further examined for the AD/normal-specific modules. Results: We obtained 30 AD-specific modules which showed gain of correlation in AD samples and 31 normal- specific modules with loss of correlation in AD samples compared to normal ones, using the network mining tool lmQCM. Functional and pathway enrichment analysis not only confirmed known gene functional categories related to AD, but also identified novel regulatory factors and pathways. Remarkably, pathway analysis suggested that a variety of viral, bacteria, and parasitic infection pathways are activated in AD samples.
    [Show full text]
  • The Use of Genetic Analyses and Functional Assays for the Interpretation of Rare Variants in Pediatric Heart Disease
    The use of genetic analyses and functional assays for the interpretation of rare variants in pediatric heart disease A dissertation submitted to the Division of Graduate Studies and Research, University of Cincinnati in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Molecular Genetics by Jeffrey A. Schubert Bachelor of Science, Mount St. Joseph University, 2012 Committee Chair: Stephanie M. Ware, M.D., Ph.D. Edmund Choi, Ph.D. Benjamin Landis, M.D. Anil Menon, Ph.D. David Wieczorek, Ph.D. Molecular Genetics, Biochemistry, and Microbiology Graduate Program College of Medicine, University of Cincinnati Cincinnati, Ohio, USA, 2018 ABSTRACT The use of next generation technologies such as whole exome sequencing (WES) has paved the way for discovering novel causes of Mendelian diseases. This has been demonstrated in pediatric heart diseases, including cardiomyopathy (CM) and familial thoracic aortic aneurysm (TAA). Each of these conditions carries a high risk of a serious cardiac event, including sudden heart failure or aortic rupture, which are often fatal. Patients with either disease can be asymptomatic before presenting with these events, which necessitates early diagnosis. Though there are many known genetic causes of disease for both conditions, there is still room for discovery of novel pathogenic genes and variants, as many patients have an undefined genetic diagnosis. WES covers the protein-coding portion of the genome, which yields a massive amount of data, though it comprises only 1% of the genome. Sorting and filtering sequencing information to identify (sometimes) a single base pair change responsible for the patient phenotype is challenging. Further, interpreting identified candidate variants must be done according to strict standards, which makes it difficult to definitively say whether a coding change is pathogenic or benign.
    [Show full text]
  • WO 2016/040794 Al 17 March 2016 (17.03.2016) P O P C T
    (12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number (43) International Publication Date WO 2016/040794 Al 17 March 2016 (17.03.2016) P O P C T (51) International Patent Classification: AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, C12N 1/19 (2006.01) C12Q 1/02 (2006.01) BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DK, DM, C12N 15/81 (2006.01) C07K 14/47 (2006.01) DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, HR, HU, ID, IL, IN, IR, IS, JP, KE, KG, KN, KP, KR, (21) International Application Number: KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, MG, PCT/US20 15/049674 MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, OM, (22) International Filing Date: PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, SC, 11 September 2015 ( 11.09.201 5) SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. (25) Filing Language: English (84) Designated States (unless otherwise indicated, for every (26) Publication Language: English kind of regional protection available): ARIPO (BW, GH, (30) Priority Data: GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, ST, SZ, 62/050,045 12 September 2014 (12.09.2014) US TZ, UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, RU, TJ, TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, (71) Applicant: WHITEHEAD INSTITUTE FOR BIOMED¬ DK, EE, ES, FI, FR, GB, GR, HR, HU, IE, IS, IT, LT, LU, ICAL RESEARCH [US/US]; Nine Cambridge Center, LV, MC, MK, MT, NL, NO, PL, PT, RO, RS, SE, SI, SK, Cambridge, Massachusetts 02142-1479 (US).
    [Show full text]
  • Human-Specific Tandem Repeat Expansion and Differential Gene Expression During Primate Evolution
    Human-specific tandem repeat expansion and differential gene expression during primate evolution Arvis Sulovaria, Ruiyang Lia, Peter A. Audanoa, David Porubskya, Mitchell R. Vollgera, Glennis A. Logsdona, Human Genome Structural Variation Consortium1, Wesley C. Warrenb, Alex A. Pollenc, Mark J. P. Chaissona,d, and Evan E. Eichlera,e,2 aDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195; bBond Life Sciences Center, University of Missouri, Columbia, MO 65201; cDepartment of Neurology, University of California, San Francisco, CA 94143; dQuantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089; and eHoward Hughes Medical Institute, University of Washington, Seattle, WA 98195 Edited by Stephen T. Warren, Emory University School of Medicine, Atlanta, GA, and approved October 1, 2019 (received for review July 17, 2019) Short tandem repeats (STRs) and variable number tandem repeats Despite their established importance in population genetics (VNTRs) are important sources of natural and disease-causing and disease association, tandem repeats, particularly VNTRs, variation, yet they have been problematic to resolve in reference are among the least characterized forms of genetic variation in genomes and genotype with short-read technology. We created a the human genome (13, 14). Their repetitive nature and some- framework to model the evolution and instability of STRs and VNTRs times extreme GC content make them particularly challenging to in apes. We phased and assembled 3 ape genomes (chimpanzee, sequence and assemble with standard whole-genome shotgun gorilla, and orangutan) using long-read and 10x Genomics linked- sequencing assembly strategies, including next generation se- read sequence data for 21,442 human tandem repeats discovered in quencing approaches that depend on bridge amplification (15).
    [Show full text]