DOCSLIB.ORG

Mouse Clasp2 Knockout Project (CRISPR/Cas9)

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Mouse Clasp2 Knockout Project (CRISPR/Cas9) https://www.alphaknockout.com Mouse Clasp2 Knockout Project (CRISPR/Cas9) Objective: To create a Clasp2 knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering. Strategy summary: The Clasp2 gene (NCBI Reference Sequence: NM_001286602 ; Ensembl: ENSMUSG00000033392 ) is located on Mouse chromosome 9. 34 exons are identified, with the ATG start codon in exon 1 and the TAG stop codon in exon 34 (Transcript: ENSMUST00000163895). Exon 3~5 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: Targeted deletion of this gene leads to impaired formation of stable microtubules in a wound healing assay, and results in a 2-fold reduction of directionally persistent migration in mutant embryonic fibroblasts. Exon 3 starts from about 4.64% of the coding region. Exon 3~5 covers 8.14% of the coding region. The size of effective KO region: ~9045 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 3 4 5 34 Legends Exon of mouse Clasp2 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 3 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 5 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(31.6% 632) | C(19.4% 388) | T(29.15% 583) | G(19.85% 397) Note: The 2000 bp section upstream of Exon 3 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(32.25% 645) | C(18.7% 374) | T(27.3% 546) | G(21.75% 435) Note: The 2000 bp section downstream of Exon 5 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% chr9 + 113833176 113835175 2000 browser details YourSeq 148 1219 1409 2000 89.1% chr14 - 60553349 60553554 206 browser details YourSeq 145 1219 1406 2000 90.1% chr16 - 37693744 37693932 189 browser details YourSeq 144 1219 1411 2000 85.8% chr10 - 40585865 40586054 190 browser details YourSeq 142 1219 1401 2000 89.1% chr9 - 86996337 86996521 185 browser details YourSeq 142 1218 1400 2000 90.9% chr6 + 86408386 86408574 189 browser details YourSeq 142 1219 1411 2000 84.8% chr13 + 96834602 96834791 190 browser details YourSeq 142 1208 1414 2000 84.5% chr1 + 63158373 63158577 205 browser details YourSeq 141 1219 1401 2000 89.1% chr1 - 74581928 74582112 185 browser details YourSeq 139 1216 1557 2000 79.7% chr1 - 93400101 93400288 188 browser details YourSeq 138 1212 1418 2000 84.8% chr1 - 172031929 172032141 213 browser details YourSeq 138 1219 1401 2000 88.0% chr1 - 77362305 77362489 185 browser details YourSeq 137 1222 1400 2000 87.1% chr9 - 119377419 119377596 178 browser details YourSeq 136 1218 1405 2000 84.0% chr15 + 93226379 93226553 175 browser details YourSeq 135 1216 1401 2000 84.7% chr5 - 65541375 65541553 179 browser details YourSeq 135 1249 1595 2000 89.5% chr13 + 58470478 58471085 608 browser details YourSeq 134 1218 1406 2000 84.0% chr18 + 88756007 88756193 187 browser details YourSeq 133 1218 1391 2000 85.9% chr10 - 79839667 79839836 170 browser details YourSeq 133 1218 1400 2000 87.6% chr10 + 117394801 117394984 184 browser details YourSeq 131 1214 1401 2000 84.7% chr19 - 7250042 7250221 180 Note: The 2000 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 2000 1 2000 2000 100.0% chr9 + 113844221 113846220 2000 browser details YourSeq 235 1131 1594 2000 89.6% chr3 - 95333347 95920492 587146 browser details YourSeq 234 1131 1610 2000 83.9% chr4 - 130689475 130689848 374 browser details YourSeq 234 1155 1610 2000 89.2% chr18 + 56380507 56546623 166117 browser details YourSeq 233 1139 1599 2000 85.3% chr18 - 6335885 6336316 432 browser details YourSeq 226 1134 1603 2000 83.5% chr2 - 179889876 179890248 373 browser details YourSeq 222 1145 1533 2000 90.0% chr12 - 111279696 111280275 580 browser details YourSeq 216 1139 1575 2000 88.5% chrX + 100630820 100631359 540 browser details YourSeq 214 1138 1590 2000 84.1% chr11 - 97430767 97431192 426 browser details YourSeq 213 1139 1588 2000 84.3% chr3 - 141992986 141993280 295 browser details YourSeq 212 1164 1590 2000 86.0% chr13 - 12513122 12513527 406 browser details YourSeq 202 1130 1579 2000 82.3% chr15 - 67340082 67340420 339 browser details YourSeq 199 1170 1599 2000 92.4% chr11 - 62469892 62470532 641 browser details YourSeq 188 1155 1599 2000 81.2% chr13 + 62608109 62608421 313 browser details YourSeq 183 1155 1599 2000 85.1% chr3 + 95864036 95864386 351 browser details YourSeq 182 1134 1605 2000 88.5% chr11 + 80412349 80412821 473 browser details YourSeq 181 1196 1604 2000 88.8% chr14 - 45535397 45536081 685 browser details YourSeq 180 1202 1581 2000 90.9% chr14 + 54593917 54872662 278746 browser details YourSeq 178 1196 1590 2000 89.5% chr5 - 123706343 123706908 566 browser details YourSeq 175 1172 1605 2000 83.4% chr17 - 27658183 27658594 412 Note: The 2000 bp section downstream of Exon 5 is BLAT searched against the genome. No significant similarity is found. Page 5 of 9 https://www.alphaknockout.com Gene and protein information: Clasp2 CLIP associating protein 2 [ Mus musculus (house mouse) ] Gene ID: 76499, updated on 24-Oct-2019 Gene summary Official Symbol Clasp2 provided by MGI Official Full Name CLIP associating protein 2 provided by MGI Primary source MGI:MGI:1923749 See related Ensembl:ENSMUSG00000033392 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 C77448; mKIAA0627; CLASP2beta; 1500004F14Rik; 8030404L10Rik Expression Broad expression in CNS E18 (RPKM 23.3), cerebellum adult (RPKM 19.0) and 21 other tissues See more Orthologs human all Genomic context Location: 9; 9 F3 See Clasp2 in Genome Data Viewer Exon count: 49 Annotation release Status Assembly Chr Location 108 current GRCm38.p6 (GCF_000001635.26) 9 NC_000075.6 (113740077..113919697) Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 9 NC_000075.5 (113650591..113828815) Chromosome 9 - NC_000075.6 Page 6 of 9 https://www.alphaknockout.com Transcript information: This gene has 11 transcripts Gene: Clasp2 ENSMUSG00000033392 Description CLIP associating protein 2 [Source:MGI Symbol;Acc:MGI:1923749] Gene Synonyms 1500004F14Rik, 8030404L10Rik, CLASP2, CLASP2alpha, CLASP2beta, CLASP2gamma Location Chromosome 9: 113,741,473-113,919,682 forward strand. GRCm38:CM001002.2 About this gene This gene has 11 transcripts (splice variants), 217 orthologues, 3 paralogues, is a member of 1 Ensembl protein family and is associated with 2 phenotypes. Transcripts Name Transcript ID bp Protein Translation ID Biotype CCDS UniProt Flags Clasp2- ENSMUST00000111838.9 5609 1286aa ENSMUSP00000107469.2 Protein coding CCDS52948 E9Q8N5 TSL:1 201 GENCODE basic APPRIS ALT1 Clasp2- ENSMUST00000166734.9 4108 1287aa ENSMUSP00000130201.2 Protein coding CCDS40787 Q08EB6 TSL:5 203 GENCODE basic APPRIS P3 Clasp2- ENSMUST00000214522.1 4159 1304aa ENSMUSP00000149670.1 Protein coding - Q08EB5 TSL:1 207 GENCODE basic APPRIS ALT1 Clasp2- ENSMUST00000163895.2 4112 1307aa ENSMUSP00000128460.2 Protein coding - F7DCH5 TSL:5 202 GENCODE basic APPRIS ALT1 Clasp2- ENSMUST00000213663.1 2727 600aa ENSMUSP00000150145.1 Protein coding - A0A1L1ST22 TSL:5 204 GENCODE basic Clasp2- ENSMUST00000216817.1 2234 400aa ENSMUSP00000150741.1 Protein coding - Q8BSE7 TSL:1 211 GENCODE basic Clasp2- ENSMUST00000215022.1 4125 103aa ENSMUSP00000149685.1 Nonsense mediated - A0A1L1SRY3 TSL:5 209 decay Clasp2- ENSMUST00000213902.1 4655 No - Retained intron - - TSL:1 205 protein Clasp2- ENSMUST00000214860.1 2773 No - Retained intron - - TSL:1 208 protein Clasp2- ENSMUST00000216280.1 1927 No - lncRNA - - TSL:1 210 protein Clasp2- ENSMUST00000213966.1 1487 No - lncRNA - - TSL:1 206 protein Page 7 of 9 https://www.alphaknockout.com 198.21 kb Forward strand 113.75Mb 113.80Mb 113.85Mb 113.90Mb Genes (Comprehensive set... Clasp2-204 >protein coding Clasp2-211 >protein coding Clasp2-210
Load more

Recommended publications
  • Analysis of Trans Esnps Infers Regulatory Network Architecture
    Analysis of trans eSNPs infers regulatory network architecture Anat Kreimer Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Graduate School of Arts and Sciences COLUMBIA UNIVERSITY 2014 © 2014 Anat Kreimer All rights reserved ABSTRACT Analysis of trans eSNPs infers regulatory network architecture Anat Kreimer eSNPs are genetic variants associated with transcript expression levels. The characteristics of such variants highlight their importance and present a unique opportunity for studying gene regulation. eSNPs affect most genes and their cell type specificity can shed light on different processes that are activated in each cell. They can identify functional variants by connecting SNPs that are implicated in disease to a molecular mechanism. Examining eSNPs that are associated with distal genes can provide insights regarding the inference of regulatory networks but also presents challenges due to the high statistical burden of multiple testing. Such association studies allow: simultaneous investigation of many gene expression phenotypes without assuming any prior knowledge and identification of unknown regulators of gene expression while uncovering directionality. This thesis will focus on such distal eSNPs to map regulatory interactions between different loci and expose the architecture of the regulatory network defined by such interactions. We develop novel computational approaches and apply them to genetics-genomics data in human. We go beyond pairwise interactions to define network motifs, including regulatory modules and bi-fan structures, showing them to be prevalent in real data and exposing distinct attributes of such arrangements. We project eSNP associations onto a protein-protein interaction network to expose topological properties of eSNPs and their targets and highlight different modes of distal regulation.
    [Show full text]
  • The Molecular Genetic Architecture of Attention Deficit Hyperactivity Disorder
    Molecular Psychiatry (2015) 20, 289–297 © 2015 Macmillan Publishers Limited All rights reserved 1359-4184/15 www.nature.com/mp EXPERT REVIEW The molecular genetic architecture of attention deficit hyperactivity disorder Z Hawi1, TDR Cummins1, J Tong1, B Johnson1, R Lau1, W Samarrai2 and MA Bellgrove1 Attention deficit hyperactivity disorder (ADHD) is a common childhood behavioral condition which affects 2–10% of school age children worldwide. Although the underlying molecular mechanism for the disorder is poorly understood, familial, twin and adoption studies suggest a strong genetic component. Here we provide a state-of-the-art review of the molecular genetics of ADHD incorporating evidence from candidate gene and linkage designs, as well as genome-wide association (GWA) studies of common single-nucleotide polymorphisms (SNPs) and rare copy number variations (CNVs). Bioinformatic methods such as functional enrichment analysis and protein–protein network analysis are used to highlight biological processes of likely relevance to the aetiology of ADHD. Candidate gene associations of minor effect size have been replicated across a number of genes including SLC6A3, DRD5, DRD4, SLC6A4, LPHN3, SNAP-25, HTR1B, NOS1 and GIT1. Although case-control SNP-GWAS have had limited success in identifying common genetic variants for ADHD that surpass critical significance thresholds, quantitative trait designs suggest promising associations with Cadherin13 and glucose–fructose oxidoreductase domain 1 genes. Further, CNVs mapped to glutamate receptor genes (GRM1, GRM5, GRM7 and GRM8) have been implicated in the aetiology of the disorder and overlap with bioinformatic predictions based on ADHD GWAS SNP data regarding enriched pathways. Although increases in sample size across multi-center cohorts will likely yield important new results, we advocate that this must occur in parallel with a shift away from categorical case-control approaches that view ADHD as a unitary construct, towards dimensional approaches that incorporate endophenotypes and statistical classification methods.
    [Show full text]
  • 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]
  • MACF1 Regulates the Migration of Pyramidal Neurons Via Microtubule Dynamics and GSK-3 Signaling
    Developmental Biology 395 (2014) 4–18 Contents lists available at ScienceDirect Developmental Biology journal homepage: www.elsevier.com/locate/developmentalbiology MACF1 regulates the migration of pyramidal neurons via microtubule dynamics and GSK-3 signaling Minhan Ka a, Eui-Man Jung a, Ulrich Mueller b, Woo-Yang Kim a,n a Developmental Neuroscience, Munroe-Meyer Institute, University of Nebraska Medical Center, Omaha, NE 68198, United States b Dorris Neuroscience Center and Department of Cell Biology, The Scripps Research Institute, La Jolla, CA 92037, United States article info abstract Article history: Neuronal migration and subsequent differentiation play critical roles for establishing functional neural Received 5 June 2014 circuitry in the developing brain. However, the molecular mechanisms that regulate these processes are Received in revised form poorly understood. Here, we show that microtubule actin crosslinking factor 1 (MACF1) determines 13 August 2014 neuronal positioning by regulating microtubule dynamics and mediating GSK-3 signaling during brain Accepted 5 September 2014 development. First, using MACF1 floxed allele mice and in utero gene manipulation, we find that MACF1 Available online 16 September 2014 deletion suppresses migration of cortical pyramidal neurons and results in aberrant neuronal positioning Keywords: in the developing brain. The cell autonomous deficit in migration is associated with abnormal dynamics of MACF1 leading processes and centrosomes. Furthermore, microtubule stability is severely damaged in neurons Neuronal migration lacking MACF1, resulting in abnormal microtubule dynamics. Finally, MACF1 interacts with and mediates Cytoskeleton GSK-3 signaling in developing neurons. Our findings establish a cellular mechanism underlying neuronal Microtubule GSK-3 migration and provide insights into the regulation of cytoskeleton dynamics in developing neurons.
    [Show full text]
  • ADHD) Gene Networks in Children of Both African American and European American Ancestry
    G C A T T A C G G C A T genes Article Rare Recurrent Variants in Noncoding Regions Impact Attention-Deficit Hyperactivity Disorder (ADHD) Gene Networks in Children of both African American and European American Ancestry Yichuan Liu 1 , Xiao Chang 1, Hui-Qi Qu 1 , Lifeng Tian 1 , Joseph Glessner 1, Jingchun Qu 1, Dong Li 1, Haijun Qiu 1, Patrick Sleiman 1,2 and Hakon Hakonarson 1,2,3,* 1 Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA; [email protected] (Y.L.); [email protected] (X.C.); [email protected] (H.-Q.Q.); [email protected] (L.T.); [email protected] (J.G.); [email protected] (J.Q.); [email protected] (D.L.); [email protected] (H.Q.); [email protected] (P.S.) 2 Division of Human Genetics, Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA 3 Department of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA * Correspondence: [email protected]; Tel.: +1-267-426-0088 Abstract: Attention-deficit hyperactivity disorder (ADHD) is a neurodevelopmental disorder with poorly understood molecular mechanisms that results in significant impairment in children. In this study, we sought to assess the role of rare recurrent variants in non-European populations and outside of coding regions. We generated whole genome sequence (WGS) data on 875 individuals, Citation: Liu, Y.; Chang, X.; Qu, including 205 ADHD cases and 670 non-ADHD controls. The cases included 116 African Americans H.-Q.; Tian, L.; Glessner, J.; Qu, J.; Li, (AA) and 89 European Americans (EA), and the controls included 408 AA and 262 EA.
    [Show full text]
  • Noncoding Rnas As Novel Pancreatic Cancer Targets
    NONCODING RNAS AS NOVEL PANCREATIC CANCER TARGETS by Amy Makler A Thesis Submitted to the Faculty of The Charles E. Schmidt College of Science In Partial Fulfillment of the Requirements for the Degree of Master of Science Florida Atlantic University Boca Raton, FL August 2018 Copyright 2018 by Amy Makler ii ACKNOWLEDGEMENTS I would first like to thank Dr. Narayanan for his continuous support, constant encouragement, and his gentle, but sometimes critical, guidance throughout the past two years of my master’s education. His faith in my abilities and his belief in my future success ensured I continue down this path of research. Working in Dr. Narayanan’s lab has truly been an unforgettable experience as well as a critical step in my future endeavors. I would also like to extend my gratitude to my committee members, Dr. Binninger and Dr. Jia, for their support and suggestions regarding my thesis. Their recommendations added a fresh perspective that enriched our initial hypothesis. They have been indispensable as members of my committee, and I thank them for their contributions. My parents have been integral to my successes in life and their support throughout my education has been crucial. They taught me to push through difficulties and encouraged me to pursue my interests. Thank you, mom and dad! I would like to thank my boyfriend, Joshua Disatham, for his assistance in ensuring my writing maintained a logical progression and flow as well as his unwavering support. He was my rock when the stress grew unbearable and his encouraging words kept me pushing along.
    [Show full text]
  • Several Fusion Genes Identified in a Spermatic Cord Leiomyoma With
    CANCER GENOMICS & PROTEOMICS 18 : 531-542 (2021) doi:10.21873/cgp.20278 Several Fusion Genes Identified in a Spermatic Cord Leiomyoma With Rearrangements of Chromosome Arms 3p and 21q IOANNIS PANAGOPOULOS 1, LUDMILA GORUNOVA 1, KRISTIN ANDERSEN 1, INGVILD LOBMAIER 2 and SVERRE HEIM 1,3 1Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway; 2Department of Pathology, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway; 3Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway Abstract. Background/Aim: Benign smooth-muscle tumors, Leiomyomas are benign smooth -muscle tumors . They have leiomyomas, occur in nearly every organ but are most been described in nearly every organ but are most common common in the uterus. Whereas much is known about the in the uterus (fibroids) (1-5). genetics of uterine leiomyomas, little genetic information Much is known about the genetics , and hence the exists about leiomyomas of other organs. Here, we report pathogenesis, of uterine leiomyomas (6-9). In brief, most and discuss the genetic findings in a para-testicular uterine leiomyomas are cytogenetically characterized by the leiomyoma. Materials and Methods: Cytogenetic, array presence of one or more of the following cytogenetic comparative genomic hybridization (aCGH) RNA aberrations: t(12;14)(q15;q23–24) ; del(7)(q21.2q31.2) ; sequencing, reverse-transcription polymerase chain reaction rearrangements involving 6p21, 10q 22, and 1p ; trisomy 12 ; (RT- PCR), and Sanger sequencing analyses were performed deletions of 3q ; and changes of the X chromosome (10, 11). on a leiomyoma of the spermatic cord removed from a 61- These chromosomal aberrations rearrange and deregulate year-old man.
    [Show full text]
  • High-Throughput Loss-Of-Heterozygosity Study of Chromosome 3P in Lung Cancer Using Single-Nucleotide Polymorphism Markers
    Research Article High-throughput Loss-of-Heterozygosity Study of Chromosome 3p in Lung Cancer Using Single-Nucleotide Polymorphism Markers Amy L.S. Tai,1 William Mak,4 Phoebe K.M. Ng,4 Daniel T.T. Chua,1 Mandy Y.M. Ng,4 Li Fu,1 Kevin K.W. Chu,1 Yan Fang,5 You Qiang Song,2,4 Muhan Chen,1 Minyue Zhang,1 Pak C. Sham,3,4 and Xin-Yuan Guan1,5 Departments of 1Clinical Oncology, 2Biochemistry, and 3Psychiatry, 4Genome Research Center, The University of Hong Kong, Hong Kong, China and 5State Key Laboratory of Oncology in Southern China, Cancer Center, Sun Yat-Sen University, Guangzhou, China Abstract candidate TSGs, such as FHIT (7), RASSF1A (8), CACNA2D2 (9), and Loss of DNA copy number at the short arm of chromosome 3 is DLC1 (10), have been widely studied. However, comparative one of the most common genetic changes in human lung genomic hybridization results showed that the loss of 3p was often involved in the whole short arm in NSCLCs (5, 11). Therefore, cancer, suggesting the existence of one or more tumor suppressor genes (TSG) at 3p. To identify most frequently the existence of some unknown TSGs at loci other than 3p21.3 and deleted regions and candidate TSGs within these regions, 3p14.2 regions is likely. a recently developed single-nucleotide polymorphism (SNP)- Conventional LOH uses limited microsatellite polymorphism mass spectrometry-genotyping (SMSG) technology was ap- markers (12), which is a time-consuming process with low- pliedto investigate the loss of heterozygosity (LOH) in 30 resolution genotyping. In addition, it is difficult to automate this primary non–small-cell lung cancers.
    [Show full text]
  • CLASP2 Antibody (C-Term) Affinity Purified Rabbit Polyclonal Antibody (Pab) Catalog # Ap7181b
    10320 Camino Santa Fe, Suite G San Diego, CA 92121 Tel: 858.875.1900 Fax: 858.622.0609 CLASP2 Antibody (C-term) Affinity Purified Rabbit Polyclonal Antibody (Pab) Catalog # AP7181b Specification CLASP2 Antibody (C-term) - Product Information Application WB, IHC-P,E Primary Accession O75122 Other Accession NP_055912 Reactivity Human Host Rabbit Clonality Polyclonal Isotype Rabbit Ig Calculated MW 141064 Antigen Region 946-975 CLASP2 Antibody (C-term) - Additional Information Gene ID 23122 Western blot analysis of anti-CLASP2 Other Names Antibody (C-term) (Cat. #AP7181b) in mouse CLIP-associating protein 2, Cytoplasmic kidney tissue lysates (35ug/lane). linker-associated protein 2, Protein Orbit CLASP2(arrow) was detected using the homolog 2, hOrbit2, CLASP2, KIAA0627 purified Pab. Target/Specificity This CLASP2 antibody is generated from rabbits immunized with a KLH conjugated synthetic peptide between 946-975 amino acids from the C-terminal region of human CLASP2. Dilution WB~~1:1000 IHC-P~~1:50~100 Format Purified polyclonal antibody supplied in PBS with 0.09% (W/V) sodium azide. This Formalin-fixed and paraffin-embedded antibody is purified through a protein A human Hepatocellular carcinoma reacted column, followed by peptide affinity with anti-CLASP2 Antibody (C-term), which purification. was peroxidase-conjugated to the secondary antibody, followed by DAB staining. This data Storage demonstrates the use of this antibody for Maintain refrigerated at 2-8°C for up to 2 immunohistochemistry; clinical relevance has weeks. For long term storage store at -20°C not been evaluated. in small aliquots to prevent freeze-thaw cycles. CLASP2 Antibody (C-term) - Background Precautions Page 1/3 10320 Camino Santa Fe, Suite G San Diego, CA 92121 Tel: 858.875.1900 Fax: 858.622.0609 CLASP2 Antibody (C-term) is for research Microtubule plus-end tracking protein that use only and not for use in diagnostic or promotes the stabilization of dynamic therapeutic procedures.
    [Show full text]
  • Establishing an Osteosarcoma Associated Protein-Protein Interaction Network to Explore the Pathogenesis of Osteosarcoma Rk to Ex
    Deng et al. European Journal of Medical Research 2013, 18:57 http://www.eurjmedres.com/content/18/1/57 EUROPEAN JOURNAL OF MEDICAL RESEARCH RESEARCH Open Access Establishing an osteosarcoma associated protein-protein interaction network to explore the pathogenesis of osteosarcoma Bi-Yong Deng, Ying-Qi Hua* and Zheng-Dong Cai* Abstract Background: The aim of this study was to establish an osteosarcoma (OS) associated protein-protein interaction network and explore the pathogenesis of osteosarcoma. Methods: The gene expression profile GSE9508 was downloaded from the Gene Expression Omnibus database, including five samples of non-malignant bone (the control), seven samples for non-metastatic patients (six of which were analyzed in duplicate), and 11 samples for metastatic patients (10 of which were analyzed in duplicate). Differentially expressed genes (DEGs) between osteosarcoma and control samples were identified by packages in R with the threshold of |logFC (fold change)| > 1 and false discovery rate < 0.05. Osprey software was used to construct the interaction network of DEGs, and genes at protein-protein interaction (PPI) nodes with high degrees were identified. The Database for Annotation, Visualization and Integrated Discovery and WebGestalt software were then used to perform functional annotation and pathway enrichment analyses for PPI networks, in which P < 0.05 was considered statistically significant. Results: Compared to the control samples, the expressions of 42 and 341 genes were altered in non-metastatic OS and metastatic OS samples, respectively. A total of 15 significantly enriched functions were obtained with Gene Ontology analysis (P < 0.05). The DEGs were classified and significantly enriched in three pathways, including the tricarboxylic acid cycle, lysosome and axon guidance.
    [Show full text]
  • Genome-Wide Contribution of Common Short-Tandem Repeats to Parkinson’S Disease Genetic Risk
    medRxiv preprint doi: https://doi.org/10.1101/2021.07.01.21259645; this version posted July 5, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available for use under a CC0 license. Genome-wide contribution of common Short-Tandem Repeats to Parkinson’s Disease genetic risk Bernabe I. Bustos1*, Kimberley Billingsley2*, Cornelis Blauwendraat2, J. Raphael Gibbs3, Ziv Gan-Or4,5,6, Dimitri Krainc1, Andrew B. Singleton2† and Steven J. Lubbe1†. For the International Parkinson’s Disease Genomics Consortium (IPDGC). 1) Ken and Ruth Davee Department of Neurology and Simpson Querrey Center for Neurogenetics, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA. 2) Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, USA 3) Computational Biology Group, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, USA. 4) The Neuro (Montreal Neurological Institute-Hospital), McGill University, Montréal, QC, Canada 5) Department of Human Genetics, McGill University, Montréal, QC, Canada 6) Department of Neurology and neurosurgery, McGill University, Montréal, QC, Canada *These authors contributed equally to this work 1 NOTE: This preprint reports new research that has not been certified by peer review and should not be used to guide clinical practice. medRxiv preprint doi: https://doi.org/10.1101/2021.07.01.21259645; this version posted July 5, 2021.
    [Show full text]
  • The Microtubule Skeleton and the Evolution of Neuronal Complexity in Vertebrates
    Biol. Chem. 2019; 400(9): 1163–1179 Nataliya I. Trushina, Armen Y. Mulkidjanian and Roland Brandt* The microtubule skeleton and the evolution of neuronal complexity in vertebrates https://doi.org/10.1515/hsz-2019-0149 Received February 4, 2019; accepted April 17, 2019; previously Introduction published online May 22, 2019 The complexity of the nervous system permits the devel- Abstract: The evolution of a highly developed nervous opment of sophisticated behavioral repertoires, such as system is mirrored by the ability of individual neurons to language, tool use, self-awareness, symbolic thought, develop increased morphological complexity. As microtu- cultural learning and consciousness. The basis for the bules (MTs) are crucially involved in neuronal development, development of such a complexity is a high neuronal het- we tested the hypothesis that the evolution of complexity is erogeneity caused by neuronal diversification on the one driven by an increasing capacity of the MT system for regu- hand and a large interconnectivity between the individual lated molecular interactions as it may be implemented by neurons on the other hand (Muotri and Gage, 2006). In a higher number of molecular players and a greater ability addition, the brain constantly needs to adapt to func- of the individual molecules to interact. We performed bio- tional challenges of various kinds during development informatics analysis on different classes of components of and adulthood by a process called neural plasticity (Zilles, the vertebrate neuronal MT cytoskeleton. We show that the 1992). At a single cell level, neural plasticity involves number of orthologs of tubulin structure proteins, MT-bind- changes in the number or the strength of synaptic con- ing proteins and tubulin-sequestering proteins expanded tacts between individual neurons thereby changing the during vertebrate evolution.
    [Show full text]