DOCSLIB.ORG

Mouse Actr1b Knockout Project (CRISPR/Cas9)

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Mouse Actr1b Knockout Project (CRISPR/Cas9) https://www.alphaknockout.com Mouse Actr1b Knockout Project (CRISPR/Cas9) Objective: To create a Actr1b knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering. Strategy summary: The Actr1b gene (NCBI Reference Sequence: NM_146107 ; Ensembl: ENSMUSG00000037351 ) is located on Mouse chromosome 1. 11 exons are identified, with the ATG start codon in exon 1 and the TAA stop codon in exon 11 (Transcript: ENSMUST00000043951). Exon 1~11 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: Exon 1 starts from about 0.09% of the coding region. Exon 1~11 covers 100.0% of the coding region. The size of effective KO region: ~9773 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' 10 1 2 3 4 5 6 7 8 9 11 Legends Exon of mouse Actr1b 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 start codon 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 stop codon 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(30.45% 609) | C(23.25% 465) | T(26.65% 533) | G(19.65% 393) Note: The 2000 bp section upstream of start codon is analyzed to determine the GC content. Significant high GC-content regions are found. The gRNA site is selected outside of these high GC-content regions. Overview of the GC Content Distribution (down) Window size: 300 bp Sequence 12 Summary: Full Length(2000bp) | A(23.85% 477) | C(25.2% 504) | T(22.6% 452) | G(28.35% 567) Note: The 2000 bp section downstream of stop codon 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% chr1 - 36709854 36711853 2000 browser details YourSeq 100 82 272 2000 88.5% chr11 + 54448307 54448544 238 browser details YourSeq 97 95 270 2000 89.6% chr10 + 76987418 77020818 33401 browser details YourSeq 90 1 193 2000 76.9% chrX - 151796084 151796259 176 browser details YourSeq 89 2 234 2000 85.0% chr13 - 51795143 51795447 305 browser details YourSeq 88 95 269 2000 87.8% chr4 + 34378839 34379016 178 browser details YourSeq 85 95 276 2000 92.9% chr5 - 25757705 25757889 185 browser details YourSeq 82 16 234 2000 91.2% chr3 - 94781870 94782372 503 browser details YourSeq 81 95 204 2000 87.2% chr7 + 65650643 65650752 110 browser details YourSeq 80 95 270 2000 92.7% chr12 + 8942544 8942744 201 browser details YourSeq 78 95 234 2000 88.3% chr8 + 25310143 25310280 138 browser details YourSeq 78 95 270 2000 86.8% chr12 + 12770489 12770687 199 browser details YourSeq 76 95 572 2000 75.6% chr6 + 15360154 15360511 358 browser details YourSeq 76 95 204 2000 90.5% chr1 + 120138133 120138242 110 browser details YourSeq 75 96 234 2000 86.4% chr8 + 105962701 105962837 137 browser details YourSeq 74 95 204 2000 86.3% chr2 - 70220182 70220286 105 browser details YourSeq 73 95 275 2000 84.8% chr7 + 6279076 6279253 178 browser details YourSeq 72 110 270 2000 93.1% chr18 - 56283237 56283399 163 browser details YourSeq 72 95 182 2000 88.6% chr17 + 24858835 24858921 87 browser details YourSeq 71 97 203 2000 90.7% chr11 - 82889079 82889186 108 Note: The 2000 bp section upstream of start codon 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% chr1 - 36698079 36700078 2000 browser details YourSeq 283 165 877 2000 83.5% chr18 - 12426754 12427424 671 browser details YourSeq 30 49 88 2000 84.3% chr15 + 102140515 102140553 39 browser details YourSeq 24 1622 1648 2000 84.0% chr15 - 100699815 100699839 25 browser details YourSeq 24 699 723 2000 100.0% chr13 - 100344345 100344371 27 browser details YourSeq 24 1035 1062 2000 85.2% chr15 + 11515885 11515911 27 browser details YourSeq 24 1950 1981 2000 87.5% chr11 + 110585136 110585167 32 browser details YourSeq 23 340 362 2000 100.0% chr4 - 97812620 97812642 23 browser details YourSeq 22 1151 1172 2000 100.0% chr17 + 49319541 49319562 22 browser details YourSeq 22 175 198 2000 95.9% chr11 + 90025685 90025708 24 browser details YourSeq 21 179 199 2000 100.0% chr9 + 117208558 117208578 21 browser details YourSeq 21 1025 1045 2000 100.0% chr9 + 95851406 95851426 21 browser details YourSeq 21 830 850 2000 100.0% chr15 + 21400126 21400146 21 Note: The 2000 bp section downstream of stop codon is BLAT searched against the genome. No significant similarity is found. Page 5 of 9 https://www.alphaknockout.com Gene and protein information: Actr1b ARP1 actin-related protein 1B, centractin beta [ Mus musculus (house mouse) ] Gene ID: 226977, updated on 15-Aug-2019 Gene summary Official Symbol Actr1b provided by MGI Official Full Name ARP1 actin-related protein 1B, centractin beta provided by MGI Primary source MGI:MGI:1917446 See related Ensembl:ENSMUSG00000037351 Gene type protein coding RefSeq status PROVISIONAL Organism Mus musculus Lineage Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus Also known as Arp1b; AA960180; AI851923; 2310066K23Rik Expression Ubiquitous expression in cortex adult (RPKM 55.7), cerebellum adult (RPKM 47.4) and 28 other tissues See more Orthologs human all Genomic context Location: 1; 1 B See Actr1b in Genome Data Viewer Exon count: 12 Annotation release Status Assembly Chr Location 108 current GRCm38.p6 (GCF_000001635.26) 1 NC_000067.6 (36698114..36710017, complement) Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 1 NC_000067.5 (36756047..36766770, complement) Chromosome 1 - NC_000067.6 Page 6 of 9 https://www.alphaknockout.com Transcript information: This gene has 7 transcripts Gene: Actr1b ENSMUSG00000037351 Description ARP1 actin-related protein 1B, centractin beta [Source:MGI Symbol;Acc:MGI:1917446] Gene Synonyms 2310066K23Rik, Arp1b Location Chromosome 1: 36,698,114-36,714,422 reverse strand. GRCm38:CM000994.2 About this gene This gene has 7 transcripts (splice variants), 106 orthologues, 27 paralogues and is a member of 1 Ensembl protein family. Transcripts Name Transcript ID bp Protein Translation ID Biotype CCDS UniProt Flags Actr1b-201 ENSMUST00000043951.9 3248 376aa ENSMUSP00000047326.3 Protein coding CCDS14887 Q8R5C5 TSL:1 GENCODE basic APPRIS P1 Actr1b-205 ENSMUST00000160084.1 728 142aa ENSMUSP00000125472.1 Protein coding - E0CZD4 CDS 3' incomplete TSL:5 Actr1b-202 ENSMUST00000159448.7 643 149aa ENSMUSP00000124343.1 Protein coding - E0CYB4 CDS 3' incomplete TSL:2 Actr1b-207 ENSMUST00000162684.2 780 No protein - Retained intron - - TSL:3 Actr1b-204 ENSMUST00000160043.1 417 No protein - Retained intron - - TSL:1 Actr1b-203 ENSMUST00000159675.1 327 No protein - Retained intron - - TSL:1 Actr1b-206 ENSMUST00000162662.1 356 No protein - lncRNA - - TSL:3 Page 7 of 9 https://www.alphaknockout.com 36.31 kb Forward strand 36.69Mb 36.70Mb 36.71Mb 36.72Mb Genes Cox5b-201 >protein coding 4933424G06Rik-201 >protein coding (Comprehensive set... Cox5b-204 >protein coding 4933424G06Rik-204 >protein coding Cox5b-206 >protein coding 4933424G06Rik-203 >retained intron Cox5b-202 >retained intron Cox5b-203 >retained intron Cox5b-205 >lncRNA Contigs < AC084389.1 Genes (Comprehensive set... < Actr1b-201protein coding < Actr1b-203retained intron< Actr1b-206lncRNA < Actr1b-207retained intron < Actr1b-202protein coding < Actr1b-205protein coding < Actr1b-204retained intron Regulatory Build 36.69Mb 36.70Mb 36.71Mb 36.72Mb Reverse strand 36.31 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 processed transcript RNA gene Page 8 of 9 https://www.alphaknockout.com Transcript: ENSMUST00000043951 < Actr1b-201protein coding Reverse strand 11.89 kb ENSMUSP00000047... Superfamily SSF53067 SMART Actin family Prints Actin family Pfam Actin family PROSITE patterns Actin/actin-like conserved site Actin, conserved site PANTHER Actin family PTHR11937:SF370 Gene3D 3.90.640.10 3.30.420.40 CDD cd00012 All sequence SNPs/i... Sequence variants (dbSNP and all other sources) Variant Legend splice region variant synonymous variant Scale bar 0 40 80 120 160 200 240 280 320 376 We wish to acknowledge the following valuable scientific information resources: Ensembl, MGI, NCBI, UCSC. Page 9 of 9.
Load more

Recommended publications
  • Seq2pathway Vignette
    seq2pathway Vignette Bin Wang, Xinan Holly Yang, Arjun Kinstlick May 19, 2021 Contents 1 Abstract 1 2 Package Installation 2 3 runseq2pathway 2 4 Two main functions 3 4.1 seq2gene . .3 4.1.1 seq2gene flowchart . .3 4.1.2 runseq2gene inputs/parameters . .5 4.1.3 runseq2gene outputs . .8 4.2 gene2pathway . 10 4.2.1 gene2pathway flowchart . 11 4.2.2 gene2pathway test inputs/parameters . 11 4.2.3 gene2pathway test outputs . 12 5 Examples 13 5.1 ChIP-seq data analysis . 13 5.1.1 Map ChIP-seq enriched peaks to genes using runseq2gene .................... 13 5.1.2 Discover enriched GO terms using gene2pathway_test with gene scores . 15 5.1.3 Discover enriched GO terms using Fisher's Exact test without gene scores . 17 5.1.4 Add description for genes . 20 5.2 RNA-seq data analysis . 20 6 R environment session 23 1 Abstract Seq2pathway is a novel computational tool to analyze functional gene-sets (including signaling pathways) using variable next-generation sequencing data[1]. Integral to this tool are the \seq2gene" and \gene2pathway" components in series that infer a quantitative pathway-level profile for each sample. The seq2gene function assigns phenotype-associated significance of genomic regions to gene-level scores, where the significance could be p-values of SNPs or point mutations, protein-binding affinity, or transcriptional expression level. The seq2gene function has the feasibility to assign non-exon regions to a range of neighboring genes besides the nearest one, thus facilitating the study of functional non-coding elements[2]. Then the gene2pathway summarizes gene-level measurements to pathway-level scores, comparing the quantity of significance for gene members within a pathway with those outside a pathway.
    [Show full text]
  • Defining Functional Interactions During Biogenesis of Epithelial Junctions
    ARTICLE Received 11 Dec 2015 | Accepted 13 Oct 2016 | Published 6 Dec 2016 | Updated 5 Jan 2017 DOI: 10.1038/ncomms13542 OPEN Defining functional interactions during biogenesis of epithelial junctions J.C. Erasmus1,*, S. Bruche1,*,w, L. Pizarro1,2,*, N. Maimari1,3,*, T. Poggioli1,w, C. Tomlinson4,J.Lees5, I. Zalivina1,w, A. Wheeler1,w, A. Alberts6, A. Russo2 & V.M.M. Braga1 In spite of extensive recent progress, a comprehensive understanding of how actin cytoskeleton remodelling supports stable junctions remains to be established. Here we design a platform that integrates actin functions with optimized phenotypic clustering and identify new cytoskeletal proteins, their functional hierarchy and pathways that modulate E-cadherin adhesion. Depletion of EEF1A, an actin bundling protein, increases E-cadherin levels at junctions without a corresponding reinforcement of cell–cell contacts. This unexpected result reflects a more dynamic and mobile junctional actin in EEF1A-depleted cells. A partner for EEF1A in cadherin contact maintenance is the formin DIAPH2, which interacts with EEF1A. In contrast, depletion of either the endocytic regulator TRIP10 or the Rho GTPase activator VAV2 reduces E-cadherin levels at junctions. TRIP10 binds to and requires VAV2 function for its junctional localization. Overall, we present new conceptual insights on junction stabilization, which integrate known and novel pathways with impact for epithelial morphogenesis, homeostasis and diseases. 1 National Heart and Lung Institute, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK. 2 Computing Department, Imperial College London, London SW7 2AZ, UK. 3 Bioengineering Department, Faculty of Engineering, Imperial College London, London SW7 2AZ, UK. 4 Department of Surgery & Cancer, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK.
    [Show full text]
  • Genetic and Genomic Analysis of Hyperlipidemia, Obesity and Diabetes Using (C57BL/6J × TALLYHO/Jngj) F2 Mice
    University of Tennessee, Knoxville TRACE: Tennessee Research and Creative Exchange Nutrition Publications and Other Works Nutrition 12-19-2010 Genetic and genomic analysis of hyperlipidemia, obesity and diabetes using (C57BL/6J × TALLYHO/JngJ) F2 mice Taryn P. Stewart Marshall University Hyoung Y. Kim University of Tennessee - Knoxville, [email protected] Arnold M. Saxton University of Tennessee - Knoxville, [email protected] Jung H. Kim Marshall University Follow this and additional works at: https://trace.tennessee.edu/utk_nutrpubs Part of the Animal Sciences Commons, and the Nutrition Commons Recommended Citation BMC Genomics 2010, 11:713 doi:10.1186/1471-2164-11-713 This Article is brought to you for free and open access by the Nutrition at TRACE: Tennessee Research and Creative Exchange. It has been accepted for inclusion in Nutrition Publications and Other Works by an authorized administrator of TRACE: Tennessee Research and Creative Exchange. For more information, please contact [email protected]. Stewart et al. BMC Genomics 2010, 11:713 http://www.biomedcentral.com/1471-2164/11/713 RESEARCH ARTICLE Open Access Genetic and genomic analysis of hyperlipidemia, obesity and diabetes using (C57BL/6J × TALLYHO/JngJ) F2 mice Taryn P Stewart1, Hyoung Yon Kim2, Arnold M Saxton3, Jung Han Kim1* Abstract Background: Type 2 diabetes (T2D) is the most common form of diabetes in humans and is closely associated with dyslipidemia and obesity that magnifies the mortality and morbidity related to T2D. The genetic contribution to human T2D and related metabolic disorders is evident, and mostly follows polygenic inheritance. The TALLYHO/ JngJ (TH) mice are a polygenic model for T2D characterized by obesity, hyperinsulinemia, impaired glucose uptake and tolerance, hyperlipidemia, and hyperglycemia.
    [Show full text]
  • Datasheet: VPA00532KT Product Details
    Datasheet: VPA00532KT Description: BETA-CENTRACTIN ANTIBODY WITH CONTROL LYSATE Specificity: BETA-CENTRACTIN Format: Purified Product Type: PrecisionAb™ Polyclonal Isotype: Polyclonal IgG Quantity: 2 Westerns Product Details Applications This product has been reported to work in the following applications. This information is derived from testing within our laboratories, peer-reviewed publications or personal communications from the originators. Please refer to references indicated for further information. For general protocol recommendations, please visit www.bio-rad-antibodies.com/protocols. Yes No Not Determined Suggested Dilution Western Blotting 1/1000 PrecisionAb antibodies have been extensively validated for the western blot application. The antibody has been validated at the suggested dilution. Where this product has not been tested for use in a particular technique this does not necessarily exclude its use in such procedures. Further optimization may be required dependant on sample type. Target Species Human Species Cross Reacts with: Mouse Reactivity N.B. Antibody reactivity and working conditions may vary between species. Product Form Purified IgG - liquid Preparation 20μl Rabbit polyclonal antibody purified by affinity chromatography Buffer Solution Phosphate buffered saline Preservative 0.09% Sodium Azide (NaN3) Stabilisers 2% Sucrose Immunogen Synthetic peptide directed towards the C terminal region of human beta-centractin External Database Links UniProt: P42025 Related reagents Entrez Gene: 10120 ACTR1B Related reagents Synonyms CTRN2 Page 1 of 3 Specificity Rabbit anti Human beta-centractin antibody recognizes beta-centractin also known as actin- related protein 1B or ACTR1B. The ACTR1B gene encodes a 42.3 kDa subunit of dynactin, a macromolecular complex consisting of 10 subunits ranging in size from 22 to 150 kDa.
    [Show full text]
  • Supplementary Materials
    Supplementary materials Supplementary Table S1: MGNC compound library Ingredien Molecule Caco- Mol ID MW AlogP OB (%) BBB DL FASA- HL t Name Name 2 shengdi MOL012254 campesterol 400.8 7.63 37.58 1.34 0.98 0.7 0.21 20.2 shengdi MOL000519 coniferin 314.4 3.16 31.11 0.42 -0.2 0.3 0.27 74.6 beta- shengdi MOL000359 414.8 8.08 36.91 1.32 0.99 0.8 0.23 20.2 sitosterol pachymic shengdi MOL000289 528.9 6.54 33.63 0.1 -0.6 0.8 0 9.27 acid Poricoic acid shengdi MOL000291 484.7 5.64 30.52 -0.08 -0.9 0.8 0 8.67 B Chrysanthem shengdi MOL004492 585 8.24 38.72 0.51 -1 0.6 0.3 17.5 axanthin 20- shengdi MOL011455 Hexadecano 418.6 1.91 32.7 -0.24 -0.4 0.7 0.29 104 ylingenol huanglian MOL001454 berberine 336.4 3.45 36.86 1.24 0.57 0.8 0.19 6.57 huanglian MOL013352 Obacunone 454.6 2.68 43.29 0.01 -0.4 0.8 0.31 -13 huanglian MOL002894 berberrubine 322.4 3.2 35.74 1.07 0.17 0.7 0.24 6.46 huanglian MOL002897 epiberberine 336.4 3.45 43.09 1.17 0.4 0.8 0.19 6.1 huanglian MOL002903 (R)-Canadine 339.4 3.4 55.37 1.04 0.57 0.8 0.2 6.41 huanglian MOL002904 Berlambine 351.4 2.49 36.68 0.97 0.17 0.8 0.28 7.33 Corchorosid huanglian MOL002907 404.6 1.34 105 -0.91 -1.3 0.8 0.29 6.68 e A_qt Magnogrand huanglian MOL000622 266.4 1.18 63.71 0.02 -0.2 0.2 0.3 3.17 iolide huanglian MOL000762 Palmidin A 510.5 4.52 35.36 -0.38 -1.5 0.7 0.39 33.2 huanglian MOL000785 palmatine 352.4 3.65 64.6 1.33 0.37 0.7 0.13 2.25 huanglian MOL000098 quercetin 302.3 1.5 46.43 0.05 -0.8 0.3 0.38 14.4 huanglian MOL001458 coptisine 320.3 3.25 30.67 1.21 0.32 0.9 0.26 9.33 huanglian MOL002668 Worenine
    [Show full text]
  • Mutation Analysis of Genes Within the Dynactin Complex in a Cohort of Hereditary Peripheral Neuropathies
    Clin Genet 2016: 90: 127–133 © 2015 John Wiley & Sons A/S. Printed in Singapore. All rights reserved Published by John Wiley & Sons Ltd CLINICAL GENETICS doi: 10.1111/cge.12712 Original Article Mutation analysis of genes within the dynactin complex in a cohort of hereditary peripheral neuropathies a a Tey S., Ahmad-Annuar A., Drew A.P., Shahrizaila N., Nicholson G.A., S. Tey , A. Ahmad-Annuar , Kennerson M.L. Mutation analysis of genes within the dynactin complex in A.P. Drewb, N. Shahrizailac, , a cohort of hereditary peripheral neuropathies. G.A. Nicholsonb d and Clin Genet 2016: 90: 127–133. © John Wiley & Sons A/S. Published by M.L. Kennersonb,d John Wiley & Sons Ltd, 2015 aDepartment of Biomedical Science, The cytoplasmic dynein–dynactin genes are attractive candidates for Faculty of Medicine, University of Malaya, b neurodegenerative disorders given their functional role in retrograde Kuala Lumpur, Malaysia, Northcott transport along neurons. The cytoplasmic dynein heavy chain (DYNC1H1) Neuroscience Laboratory, ANZAC Research Institute, and Sydney Medical gene has been implicated in various neurodegenerative disorders, and School, University of Sydney, Sydney, dynactin 1 (DCTN1) genes have been implicated in a wide spectrum of Australia, cDepartment of Medicine, disorders including motor neuron disease, Parkinson’s disease, spinobulbar Faculty of Medicine, University of Malaya, muscular atrophy and hereditary spastic paraplegia. However, the Kuala Lumpur, Malaysia, and dMolecular involvement of other dynactin genes with inherited peripheral neuropathies Medicine Laboratory, Concord Hospital, (IPN) namely, hereditary sensory neuropathy, hereditary motor neuropathy Sydney, Australia and Charcot–Marie–Tooth disease is under reported. We screened eight genes; DCTN1-6 and ACTR1A and ACTR1B in 136 IPN patients using Key words: Charcot–Marie–Tooth – whole-exome sequencing and high-resolution melt (HRM) analysis.
    [Show full text]
  • ACTR1B Antibody - C-Terminal Region Rabbit Polyclonal Antibody Catalog # AI13368
    10320 Camino Santa Fe, Suite G San Diego, CA 92121 Tel: 858.875.1900 Fax: 858.622.0609 ACTR1B antibody - C-terminal region Rabbit Polyclonal Antibody Catalog # AI13368 Specification ACTR1B antibody - C-terminal region - Product Information Application WB Primary Accession P42025 Other Accession NM_005735, NP_005726 Reactivity Human, Mouse, Rat, Rabbit, Pig, Horse, Bovine, Guinea Pig, Dog Predicted Mouse, Rat, Pig, Horse, Guinea WB Suggested Anti-ACTR1B Antibody Pig, Dog Titration: 0.2-1 μg/ml Host Rabbit Positive Control: HepG2 cell lysate Clonality Polyclonal Calculated MW 42kDa KDa ACTR1B is supported by BioGPS gene expression data to be expressed in HepG2 ACTR1B antibody - C-terminal region - Additional Information Gene ID 10120 Alias Symbol ARP1B, CTRN2, PC3 Other Names Beta-centractin, Actin-related protein 1B, ARP1B, ACTR1B, CTRN2 Format Liquid. Purified antibody supplied in 1x PBS Host:Rabbit buffer with 0.09% (w/v) sodium azide and Target Name:ACTR1B 2% sucrose. Sample Tissue:Human 721_B Antibody Dilution: 1.0μg/ml Reconstitution & Storage ACTR1B is supported by BioGPS gene Add 50 ul of distilled water. Final expression data to be expressed in 721_B anti-ACTR1B antibody concentration is 1 mg/ml in PBS buffer with 2% sucrose. For longer periods of storage, store at 20°C. Avoid repeat freeze-thaw cycles. Precautions ACTR1B antibody - C-terminal region is for research use only and not for use in diagnostic or therapeutic procedures. Page 1/3 10320 Camino Santa Fe, Suite G San Diego, CA 92121 Tel: 858.875.1900 Fax: 858.622.0609 ACTR1B antibody - C-terminal region - Protein Information Host:Rabbit Target Name:ACTR1B Sample Tissue:Human Fetal Brain Name ACTR1B Antibody Dilution: 1.0μg/ml Synonyms CTRN2 Function Component of a multi-subunit complex involved in microtubule based vesicle motility.
    [Show full text]
  • Meta-Analysis of Gene Expression in Individuals with Autism Spectrum Disorders
    Meta-analysis of Gene Expression in Individuals with Autism Spectrum Disorders by Carolyn Lin Wei Ch’ng BSc., University of Michigan Ann Arbor, 2011 A THESIS SUBMITTED IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF Master of Science in THE FACULTY OF GRADUATE AND POSTDOCTORAL STUDIES (Bioinformatics) The University of British Columbia (Vancouver) August 2013 c Carolyn Lin Wei Ch’ng, 2013 Abstract Autism spectrum disorders (ASD) are clinically heterogeneous and biologically complex. State of the art genetics research has unveiled a large number of variants linked to ASD. But in general it remains unclear, what biological factors lead to changes in the brains of autistic individuals. We build on the premise that these heterogeneous genetic or genomic aberra- tions will converge towards a common impact downstream, which might be reflected in the transcriptomes of individuals with ASD. Similarly, a considerable number of transcriptome analyses have been performed in attempts to address this question, but their findings lack a clear consensus. As a result, each of these individual studies has not led to any significant advance in understanding the autistic phenotype as a whole. The goal of this research is to comprehensively re-evaluate these expression profiling studies by conducting a systematic meta-analysis. Here, we report a meta-analysis of over 1000 microarrays across twelve independent studies on expression changes in ASD compared to unaffected individuals, in blood and brain. We identified a number of genes that are consistently differentially expressed across studies of the brain, suggestive of effects on mitochondrial function. In blood, consistent changes were more difficult to identify, despite individual studies tending to exhibit larger effects than the brain studies.
    [Show full text]
  • Genome-Wide Screening Identifies Genes and Biological Processes
    Louisiana State University LSU Digital Commons LSU Doctoral Dissertations Graduate School 10-12-2018 Genome-Wide Screening Identifies Genes and Biological Processes Implicated in Chemoresistance and Oncogene-Induced Apoptosis Tengyu Ko Louisiana State University and Agricultural and Mechanical College, [email protected] Follow this and additional works at: https://digitalcommons.lsu.edu/gradschool_dissertations Part of the Cancer Biology Commons, Cell Biology Commons, and the Genomics Commons Recommended Citation Ko, Tengyu, "Genome-Wide Screening Identifies Genes and Biological Processes Implicated in Chemoresistance and Oncogene- Induced Apoptosis" (2018). LSU Doctoral Dissertations. 4715. https://digitalcommons.lsu.edu/gradschool_dissertations/4715 This Dissertation is brought to you for free and open access by the Graduate School at LSU Digital Commons. It has been accepted for inclusion in LSU Doctoral Dissertations by an authorized graduate school editor of LSU Digital Commons. For more information, please [email protected]. GENOME-WIDE SCREENING IDENTIFIES GENES AND BIOLOGICAL PROCESSES IMPLICATED IN CHEMORESISTANCE AND ONCOGENE- INDUCED APOPTOSIS A Dissertation Submitted to the Graduate Faculty of the Louisiana State University and Agricultural and Mechanical College in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Biomedical and Veterinary Medical Sciences through the Department of Comparative Biomedical Sciences by Tengyu Ko B.S., University of California, Santa Barbara 2010 December 2018 ACKNOWLEDGEMENTS I would like to express my sincerest gratitude to my major supervisor Dr. Shisheng Li for giving me the opportunity to join his team and the freedom to pursue projects. I appreciate all of his thoughts and efforts. Truly, none of these findings would be possible without his supervisions, supports, insightful discussions, and patience.
    [Show full text]
  • Copy Number Variation in Neuropsychiatric Disorders
    UNIVERSITY OF CALIFORNIA Los Angeles Copy Number Variation in Neuropsychiatric Disorders A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Bioinformatics by Alden Yen-Wen Huang 2018 © Copyright by Alden Yen-Wen Huang 2018 ABSTRACT OF THE DISSERTATION Copy Number Variation in Neuropsychiatric Disorders by Alden Yen-Wen Huang Doctor of Philosophy in Bioinformatics University of California, Los Angeles, 2018 Professor Giovanni Coppola, Chair In this thesis, I characterize the contribution of rare copy number variation (CNV) to the genetic etiology of Tourette syndrome (TS) and bipolar disorder (BP). I accomplish this using several different study designs and various methods for CNV detection. As array data was widely available for the majority of samples evaluated, I make extensive use of this technology throughout this project and first provide an overview of the technical challenges involved and describe the analytical pipeline I developed to produce reliable CNV calls from such data. Then, in the largest TS CNV study conducted to date, I report the discovery of the first two genome-wide significant CNVs associated with the disorder, and demonstrate an increased global burden of large, singleton events and CNVs at known, pathogenic loci. Conditioned on this latter observation, I perform an exploratory analysis aimed at gene discovery through the identification of de novo copy number variants from whole-exome sequencing in a sample of affected proband, unaffected parent trios in TS. ii I then describe a CNV study of 26 large, multigenerational families with a high incidence of BP from two population isolates, using both microarray and whole-genome sequencing data.
    [Show full text]
  • ACTR1B Polyclonal Antibody
    For Research Use Only ACTR1B Polyclonal antibody Catalog Number:11023-1-AP www.ptgcn.com Catalog Number: GenBank Accession Number: Recommended Dilutions: Basic Information 11023-1-AP BC010090 WB 1:500-1:2000 Size: GeneID (NCBI): IHC 1:50-1:300 167 μg/ml 10120 IF 1:20-1:200 Source: Full Name: Rabbit ARP1 actin-related protein 1 homolog Isotype: B, centractin beta (yeast) IgG Calculated MW: Purification Method: 42 kDa Antigen affinity purification Observed MW: Immunogen Catalog Number: 42-50 kDa AG1467 Applications Tested Applications: Positive Controls: IF, IHC, WB,ELISA WB : mouse brain tissue; mouse heart Species Specificity: IHC : human breast cancer tissue; human, mouse, rat Note-IHC: suggested antigen retrieval with IF : MCF-7 cells; TE buffer pH 9.0; (*) Alternatively, antigen retrieval may be performed with citrate buffer pH 6.0 ACTR1B (also known as beta centractin) is a part of the 20S dynactin complex. It colocalizes with centrosomes and Background Information vesicular (membranous) structures and is involved in cell division. ACTR1B and ACTR1A share 90% amino acid identity, and this antibody recognizes both of ACTR1B and ACTR1A. Storage: Storage Store at -20ºC. Stable for one year after shipment. Storage Buffer: PBS with 0.02% sodium azide and 50% glycerol pH 7.3. Aliquoting is unnecessary for -20ºC storage For technical support and original validation data for this product please contact: This product is exclusively available under Proteintech T: 4006900926 E: [email protected] W: ptgcn.com Group brand and is not available to purchase from any other manufacturer. Selected Validation Data Various lysates were subjected to SDS PAGE Immunohistochemical analysis of paraffin- Immunohistochemical analysis of paraffin- followed by western blot with 11023-1-AP (ACTR1B embedded human breast cancer tissue slide using embedded human breast cancer tissue slide using antibody) at dilution of 1:1000 incubated at room 11023-1-AP (ACTR1B antibody) at dilution of 1:200 11023-1-AP (ACTR1B antibody) at dilution of 1:200 temperature for 1.5 hours.
    [Show full text]
  • ARP1 Antibody Cat
    ARP1 Antibody Cat. No.: 45-290 ARP1 Antibody Specifications HOST SPECIES: Goat SPECIES REACTIVITY: Human HOMOLOGY: Expected Species Reactivity based on sequence homology: Mouse, Dog, Pig IMMUNOGEN: The immunogen for this antibody is: C-YEEDGARSIHRKT TESTED APPLICATIONS: ELISA, WB Peptide ELISA: antibody detection limit dilution 1:1000.Western Blot:Approx. 45kDa APPLICATIONS: band observed in Human Kidney lysates (calculated MW of 42.6kDa according to NP_005727.1). Recommended concentration: 1-3ug/ml. This epitope was selected to minimise the chance of cross-reactivity with ACTR1B SPECIFICITY: (YEEDGSRAIHRKT). POSITIVE CONTROL: 1) Cat. No. 1303 - Human Brain Tissue Lysate Properties Purified from goat serum by ammonium sulphate precipitation followed by antigen PURIFICATION: affinity chromatography using the immunizing peptide. CLONALITY: Polyclonal September 23, 2021 1 https://www.prosci-inc.com/arp1-antibody-45-290.html CONJUGATE: Unconjugated PHYSICAL STATE: Liquid Supplied at 0.5 mg/ml in Tris saline, 0.02% sodium azide, pH7.3 with 0.5% bovine serum BUFFER: albumin. Aliquot and store at -20°C. Minimize freezing and thawing. CONCENTRATION: 500 ug/mL STORAGE CONDITIONS: Aliquot and store at -20˚C. Minimize freezing and thawing. Additional Info OFFICIAL SYMBOL: ACTR1A ACTR1A, ARP1, ARP1 actin-related protein 1 homolog A, centractin alpha (yeast), actin-RPV, centractin alpha, ARP1, yeast homolog A, centrosome-associated actin homolog, ARP1 ALTERNATE NAMES: (actin-related protein 1, yeast) homolog A (centractin alpha), CTRN1, FLJ52695, FLJ52800, FLJ55002, ARP1 actin-related protein 1 homolog A, centractin alpha ACCESSION NO.: NP_005727.1 PROTEIN GI NO.: 5031569 GENE ID: 10121 Background and References 1) Lees-Miller JP, Helfman DM, Schroer TA.
    [Show full text]