DOCSLIB.ORG

Mouse Stradb Knockout Project (CRISPR/Cas9)

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Mouse Stradb Knockout Project (CRISPR/Cas9) https://www.alphaknockout.com Mouse Stradb Knockout Project (CRISPR/Cas9) Objective: To create a Stradb knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering. Strategy summary: The Stradb gene (NCBI Reference Sequence: NM_172656 ; Ensembl: ENSMUSG00000026027 ) is located on Mouse chromosome 1. 12 exons are identified, with the ATG start codon in exon 2 and the TAG stop codon in exon 12 (Transcript: ENSMUST00000027185). Exon 4~10 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 4 starts from about 7.5% of the coding region. Exon 4~10 covers 77.91% of the coding region. The size of effective KO region: ~7849 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 4 5 6 7 8 9 10 12 Legends Exon of mouse Stradb 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 4 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 423 bp section downstream of Exon 10 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(27.4% 548) | C(20.4% 408) | T(32.75% 655) | G(19.45% 389) Note: The 2000 bp section upstream of Exon 4 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(423bp) | A(31.21% 132) | C(22.93% 97) | T(28.13% 119) | G(17.73% 75) Note: The 423 bp section downstream of Exon 10 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 + 58983290 58985289 2000 browser details YourSeq 121 497 865 2000 80.6% chr17 + 32175484 32175711 228 browser details YourSeq 117 673 1133 2000 78.6% chr18 + 4123418 4123691 274 browser details YourSeq 106 666 870 2000 82.4% chr11 + 68736030 68736206 177 browser details YourSeq 104 697 865 2000 80.9% chr13 + 93401175 93401332 158 browser details YourSeq 103 680 867 2000 84.1% chr11 - 98406234 98406377 144 browser details YourSeq 102 689 865 2000 91.2% chr4 - 129389570 129438964 49395 browser details YourSeq 96 668 863 2000 80.0% chr11 + 74555590 74555775 186 browser details YourSeq 92 680 865 2000 81.0% chr8 + 83680469 83680641 173 browser details YourSeq 88 693 860 2000 89.7% chr6 - 58866646 58866812 167 browser details YourSeq 88 672 862 2000 81.5% chr6 + 124707485 124707654 170 browser details YourSeq 87 663 863 2000 76.5% chr11 - 20029168 20029331 164 browser details YourSeq 87 492 861 2000 91.5% chr4 + 134103241 134103620 380 browser details YourSeq 86 674 861 2000 81.0% chr17 - 24137883 24138022 140 browser details YourSeq 85 687 871 2000 78.6% chr12 + 31460423 31460597 175 browser details YourSeq 85 743 866 2000 84.5% chr11 + 105096258 105096370 113 browser details YourSeq 85 664 870 2000 83.1% chr10 + 19282779 19282979 201 browser details YourSeq 83 746 872 2000 86.5% chr14 - 56805313 56805431 119 browser details YourSeq 83 672 870 2000 83.4% chr5 + 145360883 145361053 171 browser details YourSeq 83 685 862 2000 82.6% chr12 + 80646109 80646274 166 Note: The 2000 bp section upstream of Exon 4 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 423 1 423 423 100.0% chr1 + 58993139 58993561 423 browser details YourSeq 41 194 378 423 93.7% chr4 - 111863550 111863921 372 browser details YourSeq 40 337 378 423 100.0% chr12 - 52773756 52773851 96 browser details YourSeq 31 189 248 423 64.8% chr8 - 108899336 108899372 37 browser details YourSeq 29 206 249 423 76.5% chr5 + 24465189 24465228 40 browser details YourSeq 22 307 330 423 95.9% chr6 + 112646770 112646793 24 browser details YourSeq 22 394 418 423 95.9% chr14 + 107073782 107073811 30 browser details YourSeq 21 360 380 423 100.0% chrX - 99009096 99009116 21 browser details YourSeq 21 313 335 423 95.7% chr10 + 94834931 94834953 23 browser details YourSeq 20 335 354 423 100.0% chr7 - 11402342 11402361 20 browser details YourSeq 20 335 354 423 100.0% chr7 - 11518712 11518731 20 browser details YourSeq 20 325 344 423 100.0% chr11 - 92503383 92503402 20 browser details YourSeq 20 310 329 423 100.0% chr15 + 24501559 24501578 20 browser details YourSeq 20 404 423 423 100.0% chr12 + 37639971 37639990 20 Note: The 423 bp section downstream of Exon 10 is BLAT searched against the genome. No significant similarity is found. Page 5 of 9 https://www.alphaknockout.com Gene and protein information: Stradb STE20-related kinase adaptor beta [ Mus musculus (house mouse) ] Gene ID: 227154, updated on 10-Oct-2019 Gene summary Official Symbol Stradb provided by MGI Official Full Name STE20-related kinase adaptor beta provided by MGI Primary source MGI:MGI:2144047 See related Ensembl:ENSMUSG00000026027 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 Papk; ILPIP; ILPIPA; Syradb; Als2cr2; D1Ucla2; PRO1038; AA792893; B830008M19 Expression Ubiquitous expression in CNS E18 (RPKM 16.2), heart adult (RPKM 13.5) and 28 other tissues See more Orthologs human all Genomic context Location: 1 C1.3; 1 29.2 cM See Stradb in Genome Data Viewer Exon count: 12 Annotation release Status Assembly Chr Location 108 current GRCm38.p6 (GCF_000001635.26) 1 NC_000067.6 (58973522..58995122) Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 1 NC_000067.5 (59030415..59051966) Chromosome 1 - NC_000067.6 Page 6 of 9 https://www.alphaknockout.com Transcript information: This gene has 7 transcripts Gene: Stradb ENSMUSG00000026027 Description STE20-related kinase adaptor beta [Source:MGI Symbol;Acc:MGI:2144047] Gene Synonyms Als2cr2, D1Ucla2, PRO1038 Location Chromosome 1: 58,973,522-58,995,715 forward strand. GRCm38:CM000994.2 About this gene This gene has 7 transcripts (splice variants), 208 orthologues, 35 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 Stradb- ENSMUST00000027185.10 2960 418aa ENSMUSP00000027185.4 Protein coding CCDS14981 Q8K4T3 TSL:1 201 GENCODE basic APPRIS P1 Stradb- ENSMUST00000114296.7 1348 209aa ENSMUSP00000109935.1 Protein coding - Q8K4T3 TSL:1 202 GENCODE basic Stradb- ENSMUST00000152318.1 505 129aa ENSMUSP00000137790.1 Protein coding - M0QWE6 CDS 5' 206 incomplete TSL:5 Stradb- ENSMUST00000153990.7 2534 104aa ENSMUSP00000137724.1 Nonsense mediated - M0QW98 TSL:1 207 decay Stradb- ENSMUST00000123301.7 2070 189aa ENSMUSP00000138036.1 Nonsense mediated - A0A0R4J299 TSL:1 203 decay Stradb- ENSMUST00000147637.7 3076 No - Retained intron - - TSL:1 205 protein Stradb- ENSMUST00000123965.7 1978 No - Retained intron - - TSL:1 204 protein Page 7 of 9 https://www.alphaknockout.com 42.19 kb Forward strand 58.97Mb 58.98Mb 58.99Mb 59.00Mb Genes (Comprehensive set... Stradb-201 >protein coding Stradb-207 >nonsense mediated decay Stradb-203 >nonsense mediated decay Stradb-202 >protein coding Stradb-205 >retained intron Stradb-206 >protein coding Stradb-204 >retained intron Contigs AC169382.2 > Genes < Trak2-201protein coding < C2cd6-204protein coding (Comprehensive set... < Trak2-203protein coding < C2cd6-203protein coding < Trak2-204retained intron < AC169382.1-201lncRNA Regulatory Build 58.97Mb 58.98Mb 58.99Mb 59.00Mb Reverse strand 42.19 kb Regulation Legend CTCF Enhancer Open Chromatin Promoter Promoter Flank 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: ENSMUST00000027185 22.19 kb Forward strand Stradb-201 >protein coding ENSMUSP00000027... Low complexity (Seg) Superfamily Protein kinase-like domain superfamily Pfam Protein kinase domain PROSITE profiles Protein kinase domain PANTHER PTHR24361 PTHR24361:SF382 Gene3D 3.30.200.20 CDD cd08226 All sequence SNPs/i... Sequence variants (dbSNP and all other sources) Variant Legend stop lost missense variant synonymous variant Scale bar 0 40 80 120 160 200 240 280 320 360 418 We wish to acknowledge the following valuable scientific information resources: Ensembl, MGI, NCBI, UCSC. Page 9 of 9.
Load more

Recommended publications
  • ALS2CR2 (STRADB) 406-418) Goat Polyclonal Antibody – AP08962PU-N
    OriGene Technologies, Inc. 9620 Medical Center Drive, Ste 200 Rockville, MD 20850, US Phone: +1-888-267-4436 [email protected] EU: [email protected] CN: [email protected] Product datasheet for AP08962PU-N ALS2CR2 (STRADB) 406-418) Goat Polyclonal Antibody Product data: Product Type: Primary Antibodies Applications: ELISA, IHC, WB Recommended Dilution: ELISA: 1/32000. Immunohistochemistry on Paraffin Sections: 3.75 µg/ml. Western Blot: 1 - 3 µg/ml. Reactivity: Canine, Human Host: Goat Clonality: Polyclonal Immunogen: Synthetic peptide from C-terminus of human ALS2CR2 Specificity: This antibody reacts to STE20-Related Kinase Adaptor Beta (STRADB/ALS2CR2) at aa 406-418. It is expected to recognise both human isoforms: ILPIP-alpha (NP_061041.2) and ILPIP-beta (AAF71042.1). Formulation: Tris saline buffer, pH 7.3, 0.5% BSA, 0.02% sodium azide State: Aff - Purified State: Liquid purified Ig Concentration: lot specific Purification: Immunoaffinity Chromatography Conjugation: Unconjugated Storage: Store the antibody undiluted at 2-8°C for one month or (in aliquots) at -20°C for longer. Avoid repeated freezing and thawing. Stability: Shelf life: one year from despatch. Database Link: Entrez Gene 55437 Human Q9C0K7 This product is to be used for laboratory only. Not for diagnostic or therapeutic use. View online » ©2021 OriGene Technologies, Inc., 9620 Medical Center Drive, Ste 200, Rockville, MD 20850, US 1 / 3 ALS2CR2 (STRADB) 406-418) Goat Polyclonal Antibody – AP08962PU-N Background: Amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 2, is connected to transferase/kinase activity and ATP binding, it has recently been shown to interact with XIAP, a member of the IAP (Inhibitor of Apoptosis) protein family.
    [Show full text]
  • The Dual Role of Micrornas in Colorectal Cancer Progression
    International Journal of Molecular Sciences Review The Dual Role of MicroRNAs in Colorectal Cancer Progression Lei Ding 1,2,†, Zhenwei Lan 1,2,†, Xianhui Xiong 1,2, Hongshun Ao 1,2, Yingting Feng 1,2, Huan Gu 1,2, Min Yu 1,2 and Qinghua Cui 1,2,* 1 Lab of Biochemistry & Molecular Biology, School of Life Sciences, Yunnan University, Kunming 650091, China; [email protected] (L.D.); [email protected] (Z.L.); [email protected] (X.X.); [email protected] (H.A.); [email protected] (Y.F.); [email protected] (H.G.); [email protected] (M.Y.) 2 Key Lab of Molecular Cancer Biology, Yunnan Education Department, Kunming 650091, China * Correspondence: [email protected]; Tel.: +86-871-65031412 † These authors contributed equally to this work. Received: 29 August 2018; Accepted: 13 September 2018; Published: 17 September 2018 Abstract: Colorectal cancer (CRC) is responsible for one of the major cancer incidence and mortality worldwide. It is well known that MicroRNAs (miRNAs) play vital roles in maintaining the cell development and other physiological processes, as well as, the aberrant expression of numerous miRNAs involved in CRC progression. MiRNAs are a class of small, endogenous, non-coding, single-stranded RNAs that bind to the 3’-untranslated region (30-UTR) complementary sequences of their target mRNA, resulting in mRNA degradation or inhibition of its translation as a post-transcriptional regulators. Moreover, miRNAs also can target the long non-coding RNA (lncRNA) to regulate the expression of its target genes involved in proliferation and metastasis of CRC. The functions of these dysregulated miRNAs appear to be context specific, with evidence of having a dual role in both oncogenes and tumor suppression depending on the cellular environment in which they are expressed.
    [Show full text]
  • Newly Identified Gon4l/Udu-Interacting Proteins
    www.nature.com/scientificreports OPEN Newly identifed Gon4l/ Udu‑interacting proteins implicate novel functions Su‑Mei Tsai1, Kuo‑Chang Chu1 & Yun‑Jin Jiang1,2,3,4,5* Mutations of the Gon4l/udu gene in diferent organisms give rise to diverse phenotypes. Although the efects of Gon4l/Udu in transcriptional regulation have been demonstrated, they cannot solely explain the observed characteristics among species. To further understand the function of Gon4l/Udu, we used yeast two‑hybrid (Y2H) screening to identify interacting proteins in zebrafsh and mouse systems, confrmed the interactions by co‑immunoprecipitation assay, and found four novel Gon4l‑interacting proteins: BRCA1 associated protein‑1 (Bap1), DNA methyltransferase 1 (Dnmt1), Tho complex 1 (Thoc1, also known as Tho1 or HPR1), and Cryptochrome circadian regulator 3a (Cry3a). Furthermore, all known Gon4l/Udu‑interacting proteins—as found in this study, in previous reports, and in online resources—were investigated by Phenotype Enrichment Analysis. The most enriched phenotypes identifed include increased embryonic tissue cell apoptosis, embryonic lethality, increased T cell derived lymphoma incidence, decreased cell proliferation, chromosome instability, and abnormal dopamine level, characteristics that largely resemble those observed in reported Gon4l/udu mutant animals. Similar to the expression pattern of udu, those of bap1, dnmt1, thoc1, and cry3a are also found in the brain region and other tissues. Thus, these fndings indicate novel mechanisms of Gon4l/ Udu in regulating CpG methylation, histone expression/modifcation, DNA repair/genomic stability, and RNA binding/processing/export. Gon4l is a nuclear protein conserved among species. Animal models from invertebrates to vertebrates have shown that the protein Gon4-like (Gon4l) is essential for regulating cell proliferation and diferentiation.
    [Show full text]
  • Thesis Reference
    Thesis A kinome-wide RNAi screen to identify genes controlling membrane lipid homeostasis in human cells GEHIN, Charlotte Abstract The control of lipid homeostasis is a fundamental process that allows cells to maintain the unique lipid composition of their membrane compartments and to deal with the energetic fluxes from metabolism. If most of enzymes involved in lipid metabolism are characterized, the question of the genetic control of lipid homeostasis is still outstanding. In order to find genes that control the homeostasis of membrane lipids, I combined a large-scale RNAi screen targeting the human knome with the techniques of targeted lipidomic analysis by mass spectrometry to monitor lipid changes in HeLa cells. Data analysis of the screen allowed the characterization of candidate genes involved in the control of membrane lipid homeostasis. In parallel, in the context of the NCCR Chemical Biology, I developed a robotically-assisted siRNA transfection assay and screened a library of chemicals potentially able to transfect siRNA in Human cells at least as efficiently than commercially available compounds. Reference GEHIN, Charlotte. A kinome-wide RNAi screen to identify genes controlling membrane lipid homeostasis in human cells. Thèse de doctorat : Univ. Genève, 2014, no. Sc. 4670 URN : urn:nbn:ch:unige-380353 DOI : 10.13097/archive-ouverte/unige:38035 Available at: http://archive-ouverte.unige.ch/unige:38035 Disclaimer: layout of this document may differ from the published version. 1 / 1 UNIVERSITÉ DE GENÈVE FACULTÉ DES SCIENCES
    [Show full text]
  • Association of Cnvs with Methylation Variation
    www.nature.com/npjgenmed ARTICLE OPEN Association of CNVs with methylation variation Xinghua Shi1,8, Saranya Radhakrishnan2, Jia Wen1, Jin Yun Chen2, Junjie Chen1,8, Brianna Ashlyn Lam1, Ryan E. Mills 3, ✉ ✉ Barbara E. Stranger4, Charles Lee5,6,7 and Sunita R. Setlur 2 Germline copy number variants (CNVs) and single-nucleotide polymorphisms (SNPs) form the basis of inter-individual genetic variation. Although the phenotypic effects of SNPs have been extensively investigated, the effects of CNVs is relatively less understood. To better characterize mechanisms by which CNVs affect cellular phenotype, we tested their association with variable CpG methylation in a genome-wide manner. Using paired CNV and methylation data from the 1000 genomes and HapMap projects, we identified genome-wide associations by methylation quantitative trait locus (mQTL) analysis. We found individual CNVs being associated with methylation of multiple CpGs and vice versa. CNV-associated methylation changes were correlated with gene expression. CNV-mQTLs were enriched for regulatory regions, transcription factor-binding sites (TFBSs), and were involved in long- range physical interactions with associated CpGs. Some CNV-mQTLs were associated with methylation of imprinted genes. Several CNV-mQTLs and/or associated genes were among those previously reported by genome-wide association studies (GWASs). We demonstrate that germline CNVs in the genome are associated with CpG methylation. Our findings suggest that structural variation together with methylation may affect cellular phenotype. npj Genomic Medicine (2020) 5:41 ; https://doi.org/10.1038/s41525-020-00145-w 1234567890():,; INTRODUCTION influence transcript regulation is DNA methylation, which involves The extent of genetic variation that exists in the human addition of a methyl group to cytosine residues within a CpG population is continually being characterized in efforts to identify dinucleotide.
    [Show full text]
  • Dissecting Microregulation of a Master Regulatory Network Amit U Sinha†1, Vivek Kaimal†2,4, Jing Chen2,4 and Anil G Jegga*3,4
    BMC Genomics BioMed Central Research article Open Access Dissecting microregulation of a master regulatory network Amit U Sinha†1, Vivek Kaimal†2,4, Jing Chen2,4 and Anil G Jegga*3,4 Address: 1Department of Computer Science, University of Cincinnati, Ohio, USA, 2Department of Biomedical Engineering, University of Cincinnati, Ohio, USA, 3Department of Pediatrics, University of Cincinnati College of Medicine, Ohio, USA and 4Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Ohio, USA Email: Amit U Sinha - [email protected]; Vivek Kaimal - [email protected]; Jing Chen - [email protected]; Anil G Jegga* - [email protected] * Corresponding author †Equal contributors Published: 23 February 2008 Received: 17 September 2007 Accepted: 23 February 2008 BMC Genomics 2008, 9:88 doi:10.1186/1471-2164-9-88 This article is available from: http://www.biomedcentral.com/1471-2164/9/88 © 2008 Sinha et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: The master regulator p53 tumor-suppressor protein through coordination of several downstream target genes and upstream transcription factors controls many pathways important for tumor suppression. While it has been reported that some of the p53's functions are microRNA-mediated, it is not known as to how many other microRNAs might contribute to the p53-mediated tumorigenesis. Results: Here, we use bioinformatics-based integrative approach to identify and prioritize putative p53-regulated miRNAs, and unravel the miRNA-based microregulation of the p53 master regulatory network.
    [Show full text]
  • Microrna Regulation and Human Protein Kinase Genes
    MICRORNA REGULATION AND HUMAN PROTEIN KINASE GENES REQUIRED FOR INFLUENZA VIRUS REPLICATION by LAUREN ELIZABETH ANDERSEN (Under the Direction of Ralph A. Tripp) ABSTRACT Human protein kinases (HPKs) have profound effects on cellular responses. To better understand the role of HPKs and the signaling networks that influence influenza replication, a siRNA screen of 720 HPKs was performed. From the screen, 17 “hit” HPKs (NPR2, MAP3K1, DYRK3, EPHA6, TPK1, PDK2, EXOSC10, NEK8, PLK4, SGK3, NEK3, PANK4, ITPKB, CDC2L5, CALM2, PKN3, and HK2) were validated as important for A/WSN/33 influenza virus replication, and 6 HPKs (CDC2L5, HK2, NEK3, PANK4, PLK4 and SGK3) identified as important for A/New Caledonia/20/99 influenza virus replication. Meta-analysis of the hit HPK genes identified important for influenza virus replication showed a level of overlap, most notably with the p53/DNA damage pathway. In addition, microRNAs (miRNAs) predicted to target the validated HPK genes were determined based on miRNA seed site predictions from computational analysis and then validated using a panel of miRNA agonists and antagonists. The results identify miRNA regulation of hit HPK genes identified, specifically miR-148a by targeting CDC2L5 and miR-181b by targeting SGK3, and suggest these miRNAs also have a role in regulating influenza virus replication. Together these data advance our understanding of miRNA regulation of genes critical for virus replication and are important for development novel influenza intervention strategies. INDEX WORDS: Influenza virus,
    [Show full text]
  • (12) United States Patent (10) Patent No.: US 8,178,317 B2 Roberts Et Al
    US008178317B2 (12) United States Patent (10) Patent No.: US 8,178,317 B2 Roberts et al. (45) Date of Patent: May 15, 2012 (54) COMPOSITIONS AND METHODS FOR Mende, I. et al., “Oncogenic Transformation Induced by Membrane IDENTIFYING TRANSFORMING AND Targeted AKT2 and AKT3.” Oncogene 20:4419-4423 (2001). TUMIOR SUPPRESSOR GENES Invitation to Pay Additional Fees and Partial International Search Report dated Oct. 14, 2008 from PCT/US2008/062230. (75) Inventors: Thomas M. Roberts, Cambridge, MA Bamford et al., “The COSMIC (Catalogue of Somatic Mutations in (US); Jean Zhao, Brookline, MA (US); Cancer) database and website.” British Journal of Cancer, 91:355 David E. Hill, Arlington, MA (US); 358 (2004). Bartkova et al., “Cyclin D1 protein expression and function in human William C. Hahn, Newton, MA (US); breast cancer.” Int. J. Cancer, 57(3):353-361 (1994). Jesse Boehm, Jamaica Plain, MA (US) Berger et al., “Androgen-Induced Differentiation and Tumorigenicity of Human Prostate Epithelial Cells.” Cancer Research, 64:8867-8875 (73) Assignee: Dana-Farber Cancer Institute, Inc., (2004). Boston, MA (US) Boehm et al., “Transformation of Human and Murine Fibroblasts without Viral Oncoproteins.” Molecular and Cellular Biology, *) Notice: Subject to anyy disclaimer, the term of this 25(15):6464-6474 (2005). patent is extended or adjusted under 35 Brown et al., "Control of IkappaB-alphaproteolysis by site-specific, U.S.C. 154(b) by 233 days. signal-induced phosphorylation.” Science, 267: 1485-1488 (1995). Brunet et al., “Constitutively active mutants of MAP kinase kinase (21) Appl. No.: 12/150,941 (MEK1) induce growth factor-relaxation and oncogenicity when expressed in fibroblasts.” Oncogene, 9(11):3379-3387 (1994).
    [Show full text]
  • Molecular Networks Involved in Mouse Cerebral Corticogenesis and Spatio
    Open Access Research2009LingetVolume al. 10, Issue 10, Article R104 Molecular networks involved in mouse cerebral corticogenesis and spatio-temporal regulation of Sox4 and Sox11 novel antisense transcripts revealed by transcriptome profiling King-Hwa Ling*†‡#, Chelsee A Hewitt*††, Tim Beissbarth§‡‡, Lavinia Hyde§§§, Kakoli Banerjee¶, Pike-See Cheah¶¥, Ping Z Cannon*, Christopher N Hahn#, Paul Q Thomas¶, Gordon K Smyth§, Seong-Seng Tan**, Tim Thomas* and Hamish S Scott*†# Addresses: *Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Royal Parade, Parkville, Victoria 3052, Australia. †The School of Medicine, The University of Adelaide, SA, 5005, Australia. ‡Department of Obstetrics and Gynaecology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor DE, Malaysia. §Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Royal Parade, Parkville, Victoria 3052, Australia. ¶School of Molecular and Biomedical Science, Faculty of Sciences, University of Adelaide, Adelaide, SA 5005, Australia. ¥Department of Human Anatomy, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor DE, Malaysia. #Department of Molecular Pathology, The Institute of Medical and Veterinary Science and The Hanson Institute, Adelaide, SA 5000, Australia. **Howard Florey Institute, The University of Melbourne, Parkville, Victoria 3010, Australia. ††Current address: Pathology Department, The Peter MacCallum Cancer Centre, St Andrews
    [Show full text]
  • Genome-Wide Survey of Microrna–Transcription Factor Feed-Forward Regulatory Circuits in Humanw
    View Article Online / Journal Homepage / Table of Contents for this issue PAPER www.rsc.org/molecularbiosystems | Molecular BioSystems Genome-wide survey of microRNA–transcription factor feed-forward regulatory circuits in humanw Angela Re,za Davide Cora´,zbd Daniela Tavernacd and Michele Caselle*bd Received 7th January 2009, Accepted 27th April 2009 First published as an Advance Article on the web 19th June 2009 DOI: 10.1039/b900177h In this work, we describe a computational framework for the genome-wide identification and characterization of mixed transcriptional/post-transcriptional regulatory circuits in humans. We concentrated in particular on feed-forward loops (FFL), in which a master transcription factor regulates a microRNA, and together with it, a set of joint target protein coding genes. The circuits were assembled with a two step procedure. We first constructed separately the transcriptional and post-transcriptional components of the human regulatory network by looking for conserved over-represented motifs in human and mouse promoters, and 30-UTRs. Then, we combined the two subnetworks looking for mixed feed-forward regulatory interactions, finding a total of 638 putative (merged) FFLs. In order to investigate their biological relevance, we filtered these circuits using three selection criteria: (I) GeneOntology enrichment among the joint targets of the FFL, (II) independent computational evidence for the regulatory interactions of the FFL, extracted from external databases, and (III) relevance of the FFL in cancer. Most of the
    [Show full text]
  • 1 Novel Expression Signatures Identified by Transcriptional Analysis
    ARD Online First, published on October 8, 2009 as 10.1136/ard.2009.108043 Ann Rheum Dis: first published as 10.1136/ard.2009.108043 on 7 October 2009. Downloaded from Novel expression signatures identified by transcriptional analysis of separated leukocyte subsets in SLE and vasculitis 1Paul A Lyons, 1Eoin F McKinney, 1Tim F Rayner, 1Alexander Hatton, 1Hayley B Woffendin, 1Maria Koukoulaki, 2Thomas C Freeman, 1David RW Jayne, 1Afzal N Chaudhry, and 1Kenneth GC Smith. 1Cambridge Institute for Medical Research and Department of Medicine, Addenbrooke’s Hospital, Hills Road, Cambridge, CB2 0XY, UK 2Roslin Institute, University of Edinburgh, Roslin, Midlothian, EH25 9PS, UK Correspondence should be addressed to Dr Paul Lyons or Prof Kenneth Smith, Department of Medicine, Cambridge Institute for Medical Research, Addenbrooke’s Hospital, Hills Road, Cambridge, CB2 0XY, UK. Telephone: +44 1223 762642, Fax: +44 1223 762640, E-mail: [email protected] or [email protected] Key words: Gene expression, autoimmune disease, SLE, vasculitis Word count: 2,906 The Corresponding Author has the right to grant on behalf of all authors and does grant on behalf of all authors, an exclusive licence (or non-exclusive for government employees) on a worldwide basis to the BMJ Publishing Group Ltd and its Licensees to permit this article (if accepted) to be published in Annals of the Rheumatic Diseases and any other BMJPGL products to exploit all subsidiary rights, as set out in their licence (http://ard.bmj.com/ifora/licence.pdf). http://ard.bmj.com/ on October 2, 2021 by guest. Protected copyright. 1 Copyright Article author (or their employer) 2009.
    [Show full text]
  • Polyclonal Antibody to STRAD Beta / ILPIP 406-418) - Aff - Purified
    OriGene Technologies, Inc. OriGene Technologies GmbH 9620 Medical Center Drive, Ste 200 Schillerstr. 5 Rockville, MD 20850 32052 Herford UNITED STATES GERMANY Phone: +1-888-267-4436 Phone: +49-5221-34606-0 Fax: +1-301-340-8606 Fax: +49-5221-34606-11 [email protected] [email protected] AP08962PU-N Polyclonal Antibody to STRAD beta / ILPIP 406-418) - Aff - Purified Alternate names: ALS2CR2, CALS-21, PRO1038, Pseudokinase ALS2CR2, STE20-related kinase adapter protein beta, STRADB Quantity: 50 µg Concentration: 0.5 mg/ml Background: Amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 2, is connected to transferase/kinase activity and ATP binding, it has recently been shown to interact with XIAP, a member of the IAP (Inhibitor of Apoptosis) protein family. Together, these two proteins synergistically activate the TAK1/JNK1 signal transduction pathway, which acts to protect against the interleukin-1 converting enzyme of Fas-induced apotosis. This protein was independently isolated and characterized as polyploidy-associated protein kinase (PAPK), a member of the Ste20/germinal center kinase family that modulates cytoskeletal organization and cell survival, suggesting that its protective role may be a function of its kinase activity. Although two mRNA sequences have been isolated, only the shorter isoform has been observed. Uniprot ID: Q9C0K7 NCBI: NP_001193793.1 GeneID: 55437 Host: Goat Immunogen: Synthetic peptide from C-terminus of human ALS2CR2 AA Sequence: CDFPDEKDSYWEF Remarks: Percent identity by BLAST analysis: Human, Gorilla, Gibbon, Monkey (100%); Marmoset, Bovine, Dog (92%); Panda, Rabbit, Pig (85%) Format: State: Liquid purified Ig Purification: Immunoaffinity Chromatography Buffer System: Tris saline buffer, pH 7.3, 0.5% BSA, 0.02% sodium azide Applications: ELISA: 1/32000.
    [Show full text]