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Clc dna workbench

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The CLC DNA Workbench is a software application that provides a comprehensive suite of tools for the analysis and visualization of DNA sequence data. It offers a range of features for tasks such as sequence alignment, assembly, annotation, and phylogenetic analysis.

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Lab products found in correlation

Abi 3130 genetic analyzer, by Thermo Fisher Scientific (2 mentions) Abi bigdye terminator v3.1 cycle sequencing kit, by Thermo Fisher Scientific (2 mentions) Gotaq polymerase, by Promega (2 mentions) Bigdye terminator cycle sequencing kit, by Thermo Fisher Scientific (2 mentions) Abi 3130xl genetic analyzer, by Thermo Fisher Scientific (2 mentions) Humancytosnp 12 v2.1 beadchip, by Illumina (2 mentions) Abi prism 3130xl genetic analyzer, by Thermo Fisher Scientific (1 mentions) Vector nti, by Thermo Fisher Scientific (1 mentions) Ex taq, by Takara Bio (1 mentions) Tianamp blood dna midi kit, by Tiangen Biotech (1 mentions) Lb medium, by Merck Group (1 mentions) Rhvegf165, by Thermo Fisher Scientific (1 mentions) Dneasy blood tissue kit, by Qiagen (1 mentions)

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CLC DNA workbench software version 5.7.1 CLC DNA Workbench software

9 protocols using clc dna workbench

1

PCR and Capillary Sequencing Protocol

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Primers were designed using Primer347 (link),48 (link). PCR was performed using GOTaq polymerase (Promega, Madison, WI, USA) on DNA from peripheral blood and on cDNA from lymphoblastoid cells, using standard protocol. Capillary electrophoresis sequencing (ABI 3130 genetic analyzer; Applied Biosystems, Carlsbad, CA, USA) was performed using the ABI BigDye terminator V3.1 Cycle Sequencing Kit (Applied Biosystems, Carlsbad, CA, USA), following standard protocol. Data was analysed in CLC DNA Workbench (CLC Bio, Aarhus, Denmark).
Helsmoortel C., Vulto-van Silfhout A.T., Coe B.P., Vandeweyer G., Rooms L., van den Ende J., Schuurs-Hoeijmakers J.H., Marcelis C.L., Willemsen M.H., Vissers L.E., Yntema H.G., Bakshi M., Wilson M., Witherspoon K.T., Malmgren H., Nordgren A., Annerén G., Fichera M., Bosco P., Romano C., de Vries B.B., Kleefstra T., Kooy R.F., Eichler E.E, & Van der Aa N. (2014). A SWI/SNF related autism syndrome caused by de novo mutations in ADNP. Nature genetics, 46(4), 380-384.
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2

PCR and Capillary Sequencing Protocol

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Primers were designed using Primer347 (link),48 (link). PCR was performed using GOTaq polymerase (Promega, Madison, WI, USA) on DNA from peripheral blood and on cDNA from lymphoblastoid cells, using standard protocol. Capillary electrophoresis sequencing (ABI 3130 genetic analyzer; Applied Biosystems, Carlsbad, CA, USA) was performed using the ABI BigDye terminator V3.1 Cycle Sequencing Kit (Applied Biosystems, Carlsbad, CA, USA), following standard protocol. Data was analysed in CLC DNA Workbench (CLC Bio, Aarhus, Denmark).
Helsmoortel C., Vulto-van Silfhout A.T., Coe B.P., Vandeweyer G., Rooms L., van den Ende J., Schuurs-Hoeijmakers J.H., Marcelis C.L., Willemsen M.H., Vissers L.E., Yntema H.G., Bakshi M., Wilson M., Witherspoon K.T., Malmgren H., Nordgren A., Annerén G., Fichera M., Bosco P., Romano C., de Vries B.B., Kleefstra T., Kooy R.F., Eichler E.E, & Van der Aa N. (2014). A SWI/SNF related autism syndrome caused by de novo mutations in ADNP. Nature genetics, 46(4), 380-384.
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3

Sanger Sequencing of 11q11 Genes

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OR genes involved in the 11q11 deletion were confirmed by Sanger sequencing (Genbank accession nos. AB065774, AB065775, and BK004390). Gene-specific primers were designed using Primer3 software and are available upon request (genome build GRCh37/hg19). Polymerase chain reactions (PCR) were carried out under standard conditions followed by direct sequencing of the purified PCR product on an ABI Prism Genetic Analyzer 3130xl (Applied Biosystems Inc., Foster City, CA, USA). Sequences were analyzed using CLC DNA workbench (CLC Bio, Aarhus, Denmark).
Diels S., Huybreghts S., Van Hoorenbeeck K., Massa G., Verrijken A., Verhulst S.L., Van Gaal L.F, & Van Hul W. (2020). Copy number variant analysis and expression profiling of the olfactory receptor-rich 11q11 region in obesity predisposition. Molecular Genetics and Metabolism Reports, 25, 100656.
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4

Yeast Genetic Manipulation Protocol

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Yeast cells were transformed with the LiOAc/SS-DNA/PEG method 67 (link)68 (link). Yeast genomic DNA was extracted with
Phenol/Chloroform/Isoamyl-alcohol (25:24:1) 69 (link) and further purified with ethanol precipitation if required. PCR
was performed with high-fidelity polymerases Phusion and Q5 (New England
Biolabs) or ExTaq (Takara) and Taq (New England Biolabs) for diagnostic
purposes. Sanger sequencing 70 (link) was
performed by the VIB Genetic Service Facility (Antwerp). The sequences were
analyzed with Vector NTI (Invitrogen) or CLC DNA workbench (CLC Bio) software.
Lists of primers and plasmids are provided as supplementary tables S4 and S5,
respectively.
Abt T.D., Souffriau B., Foulquié-Moreno M.R., Duitama J, & Thevelein J.M. (2016). Genomic saturation mutagenesis and polygenic analysis identify novel yeast genes affecting ethyl acetate production, a non-selectable polygenic trait. Microbial Cell, 3(4), 159-175.
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5

Genetic Analysis of BGN Exons

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Sanger sequencing of the seven coding exons of BGN (RefSeq transcript
NM_001711.3) was performed. The PCR primer sequences and reaction conditions are
listed in Supplementary Table S1 online. PCR products were bidirectionally
sequenced using the BigDye Terminator Cycle Sequencing kit (Applied Biosystems,
Carlsbad, CA) and separated on an ABI 3130XL Genetic Analyzer (Applied
Biosystems). Sequences were analyzed using CLC DNA workbench (CLC Bio, Aarhus,
Denmark). Microarray analysis was performed using the Illumina HumanCytoSNP12-V2.1
BeadChip (Illumina, San Diego, CA) according to standard protocols. Copy-number
variants (CNVs) were analyzed using CNV-WebStore.12 (link)
Meester J.A., Vandeweyer G., Pintelon I., Lammens M., Van Hoorick L., De Belder S., Waitzman K., Young L., Markham L.W., Vogt J., Richer J., Beauchesne L.M., Unger S., Superti-Furga A., Prsa M., Dhillon R., Reyniers E., Dietz H.C., Wuyts W., Mortier G., Verstraeten A., Van Laer L, & Loeys B.L. (2016). Loss-of-function mutations in the X-linked biglycan gene cause a severe syndromic form of thoracic aortic aneurysms and dissections. Genetics in Medicine, 19(4), 386-395.
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6

Sanger Sequencing and Microarray Analysis of BGN

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Sanger sequencing of the seven coding exons of BGN (RefSeq transcript NM_001711.3) was performed. The PCR primer sequences and reaction conditions are listed in Table S1. PCR products were bidirectionally sequenced using the BigDye Terminator Cycle Sequencing kit (Applied Biosystems, Carlsbad, CA) and separated on an ABI 3130XL Genetic Analyzer (Applied Biosystems, Carlsbad, CA). Sequences were analyzed using CLC DNA workbench (CLC Bio, Aarhus, Denmark). Microarray analysis was performed using the Illumina HumanCytoSNP12-V2.1 BeadChip (Illumina, San Diego, CA) according to standard protocols. Copy number variant (CNV) analysis was performed using CNV-webstore.12 (link)
Meester J.A., Vandeweyer G., Pintelon I., Lammens M., Van Hoorick L., De Belder S., Waitzman K., Young L., Markham L.W., Vogt J., Richer J., Beauchesne L.M., Unger S., Superti-Furga A., Prsa M., Dhillon R., Reyniers E., Dietz H.C., Wuyts W., Mortier G., Verstraeten A., Van Laer L, & Loeys B.L. (2016). Loss-of-function mutations in the X-linked biglycan gene cause a severe syndromic form of thoracic aortic aneurysms and dissections. Genetics in Medicine, 19(4), 386-395.
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7

Identifying LDLR Pathogenic Mutations

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We extracted genomic DNA from 500 μL of peripheral blood using a TIANamp Blood DNA Midi Kit (Tiangen, Beijing, China). After performing genomic polymerase chain reaction (PCR), we sequenced the coding exons and their flanking intronic sequences of LDLR (GenBank NM_000527.4) for pathogenic mutations in the family members. The primers used in PCR have been described in an earlier report [13 ]. We screened for mutations in LDLR by direct sequencing. To verify the mutation, we separated heterozygous alleles by cloning the affected fragment into an EGFP-N1 vector. The fragment was amplified by PCR using forward primer 5′-TGAAATCTCGATGGAGTGGGTCCCATC-3′ and reverse primer 5′-CTGTAGCTAGACCAAAATCACCTATTTTTACTG-3′ and then cloned into EGFP-N1 vector. Plasmids were extracted from colonies and sequenced using the same primer. To confirm the novel mutation in LDLR, we also examined the mutation in the 100 unrelated controls. We performed the analysis of amino acid conservation around the mutation site using a CLC DNA Workbench (QIAGEN Bioinformatics, Germany).
Shu H., Chi J., Li J., Zhang W., Lv W., Wang J., Deng Y., Hou X, & Wang Y. (2017). A novel indel variant in LDLR responsible for familial hypercholesterolemia in a Chinese family. PLoS ONE, 12(12), e0189316.
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8

Shark VEGF-Targeting Antibody Discovery

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A male Heterodontus francisci shark was immunized iv with 1 μg rhVEGF165 (Peprotech (Rocky Hill, NJ, USA), 300-01A) in 1× PBS every 15 days for 20 weeks. The dissection of the spleen, mRNA purification, and library generation were performed as described [48 (link)]. For the phage display, 3 rounds of panning were completed against 250 ng/well of rhVEGF165 with 5, 10, and 20 wash cycles with 1× PBS/0.5% Tween (PBST-0.5). Positive colonies were selected by PCR with the ompseq and gback primers [49 ]. Positive PCR clones were grown in LB medium (Sigma (St. Louis, MO, USA), L3022), and plasmids were isolated using commercial kits (Qiagen (Hilden, Germany), 27104). Their sequences were obtained by capillary electrophoresis (Seqxcel, San Diego, CA, USA), analyzed on a CLC DNA Workbench (Qiagen, version 121 7.9.0, Redwood, CA, USA), and compared with internal and external databases using NCBI BLAST.
Camacho-Villegas T.A., Mata-González M.T., García-Ubbelohd W., Núñez-García L., Elosua C., Paniagua-Solis J.F, & Licea-Navarro A.F. (2018). Intraocular Penetration of a vNAR: In Vivo and In Vitro VEGF165 Neutralization. Marine Drugs, 16(4), 113.
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9

Insect Identification in Fagus sylvatica Seeds

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For 56 out of 58 obtained seed lots, the seeds were X-rayed to reveal the presence of insects (Appendix S1: Table S1), as described by Roques and Skrzypczy nska (2003) . Two seed lots of Fagus sylvatica L. (SL 72 and SL 73) were not assessed for insects because of late delivery. Infested seeds were dissected with a dissecting knife, and insects were collected and individually stored in collection tubes with 95-99% ethanol. All larvae were examined using a microscope and were identified to order level. All seeds were also visually inspected for exit holes of insects.
Genomic DNA was extracted from individual insect specimens with DNeasy Blood & Tissue Kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions. A fragment of the mitochondrial gene (mtDNA) cytochrome oxidase c subunit 1 (COI) was subsequently amplified by PCR in 25 lL reaction volumes containing 2 lL of DNA template, 0.2 lmol/L of each of the primers LCO1490 and HCO2198 (Folmer Sequences were assembled and edited with CLC DNA Workbench (Qiagen) and compared against reference sequences in the BOLDSYSTEMS (Ratnasingham and Hebert 2007) and National Centre for Biotechnology Information (NCBI) GenBank databases (Geer et al. 2010) . The specimens' queries were matched to its best matching identified reference sequence for identification.
Franić I., Prospero S., Hartmann M., Allan E., Auger-Rozenberg M.A., Grünwald N.J., Kenis M., Roques A., Schneider S., Sniezko R., Williams W, & Eschen R. (2019). Are traded forest tree seeds a potential source of nonnative pests?. Ecological applications : a publication of the Ecological Society of America, 29(7).
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