Focused ultrasonicator

Manufactured by Covaris

Sourced in United States

The Focused-ultrasonicator is a laboratory instrument designed to perform high-intensity, focused ultrasonic processing. It utilizes focused acoustic energy to rapidly disrupt and homogenize a wide range of sample types. The core function of this equipment is to provide controlled, localized energy input for sample preparation and processing applications.

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Lab products found in correlation

Kapa hyper prep without amplification module, by Roche (6 mentions) Bravo liquid handling platform, by Agilent Technologies (5 mentions) Ampure xp bead, by Beckman Coulter (4 mentions) Bioanalyzer, by Agilent Technologies (3 mentions) Dneasy blood and tissue kit, by Qiagen (3 mentions) Agilent 2100 bioanalyzer, by Agilent Technologies (3 mentions) Spri bead, by Beckman Coulter (3 mentions) Ez dna methylation gold kit, by Zymo Research (3 mentions) Miseq run, by Illumina (2 mentions) Bclfastq 1, by Illumina (2 mentions) Qubit fluorometer, by Thermo Fisher Scientific (2 mentions) Ovation rapid dr multiplex system 1 96, by Tecan (2 mentions) Sureselect target enrichment system, by Agilent Technologies (2 mentions) Tapestation, by Agilent Technologies (2 mentions) Hiseq 1500, by Illumina (2 mentions) Hiseq sequencing system, by Illumina (2 mentions) Ovation rna seq system v2, by Tecan (2 mentions) Qiaamp dna blood mini kit, by Qiagen (2 mentions) Qiaamp dna ffpe tissue kit, by Qiagen (2 mentions) Hiseq 2000, by Illumina (2 mentions)

Spelling variants of this product

S220 Focused-ultrasonicator (205 citations) Ultrasonicator (113 citations) ME220 Focused-ultrasonicator (26 citations) LE220-plus Focused-ultrasonicator (16 citations) S220 Focused-ultrasonicator instrument (7 citations) E210 focused ultrasonicator (5 citations) S2/E210 Focused-ultrasonicator (3 citations) S-Series Focused ultrasonicator (3 citations) S2X Focused-ultrasonicator (2 citations) S200 focused ultrasonicator (2 citations)

73 protocols using focused ultrasonicator

Illumina MiSeq Library Construction

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Library construction, adapter ligation and sequencing (5 Mio. read pairs, 0.6 GB of an Illumina Miseq run) were outsourced (LGC Genomics GmbH, Berlin, Germany). After DNA fragmentation with a focusedultrasonicator (Covaris, Woburn, Massachusetts, USA) libraries were prepared using the Ovation Rapid DR Multiplex System 1-96 (NuGEN) including the following steps: end repair, ligation, final repair, library purification and library amplification (14 cycles). Libraries were pooled, purified and size selected via preparative gel electrophoresis and quality controlled using the BioAnalyzer (Agilent, Santa Clara, CA 95051, USA) and Qubit fluorometer (Thermofisher Scientific, Waltham, USA).
One sample from the accession 'Bona' was previously sequenced in a separate run to test for sequence quality and mt enrichment. The Illumina bclfastq 1.8.4 software was used for demultiplexing and quality filtering of the reads under the allowance of one or two mismatches and removal of short reads (\ 20 bases).
NGS data were deposited in Genbank (NCBI) under the following dataset: Temporary Submission ID: SUB5046906/BioProject ID: PRJNA515664.

Ruzicka J, & Novak J. (2020). Mitochondrial genome variation between different accessions of Matricaria chamomilla L. (Asteraceae) based on SNP mutation analysis. Genetic resources and crop evolution, 67(4).

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Acoustic Shearing and Indexed Library Prep

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Input genomic DNA (350 ng in 50 μL) was acoustically sheared using a Covaris focused-ultrasonicator (~385 bp fragment range). Following shearing, an additional size selection was performed using a SPRI cleanup. Library preparation was performed using KAPA Hyper Prep without amplification module (KAPA Biosystems) with palindromic forked adapters containing unique eight-base index sequences embedded within the adaptor (Integrated DNA Technologies). Libraries were quantified using quantitative PCR (KAPA Biosystems), with probes specific to the ends of the adapters. The assay was automated on the Agilent Bravo liquid handling system. Based on qPCR quantification, libraries were normalized to 1.7 nM and pooled into 24-plexes.

Clark D.J., Dhanasekaran S.M., Petralia F., Pan J., Song X., Hu Y., da Veiga Leprevost F., Reva B., Lih T.S., Chang H.Y., Ma W., Huang C., Ricketts C.J., Chen L., Krek A., Li Y., Rykunov D., Li Q.K., Chen L.S., Ozbek U., Vasaikar S., Wu Y., Yoo S., Chowdhury S., Wyczalkowski M.A., Ji J., Schnaubelt M., Kong A., Sethuraman S., Avtonomov D.M., Ao M., Colaprico A., Cao S., Cho K.C., Kalayci S., Ma S., Liu W., Ruggles K., Calinawan A., Gümüş Z.H., Geiszler D., Kawaler E., Teo G.C., Wen B., Zhang Y., Keegan S., Li K., Chen F., Edwards N., Pierorazio P.M., Chen X.S., Pavlovich C.P., Hakimi A.A., Brominski G., Hsieh J.J., Antczak A., Omelchenko T., Lubinski J., Wiznerowicz M., Linehan W.M., Kinsinger C.R., Thiagarajan M., Boja E.S., Mesri M., Hiltke T., Robles A.I., Rodriguez H., Qian J., Fenyö D., Zhang B., Ding L., Schadt E., Chinnaiyan A.M., Zhang Z., Omenn G.S., Cieslik M., Chan D.W., Nesvizhskii A.I., Wang P, & Zhang H. (2019). Integrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma. Cell, 179(4), 964-983.e31.

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Acoustic Shearing and Indexed Library Prep

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Long-read Sequencing of DNA Fragments

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DNA samples were sonicated in a Focused-ultrasonicator (Covaris) into fragments with an average size of 800–1000 bp. Library preparation was done following the manufacturer’s instructions (SureSelect Target Enrichment System for Roche 454 GS FLX and GS Junior Sequencing Platforms). SureSelect libraries were directed for SMRTbell library preparation (2 kb Template Preparation Procedure: DNA damage repair till first purification of SMRTbell templates using 0.6X AMPure PB beads) and sequenced on the Pacific Biosciences RS II machine with the P5-C3 or P6-C4 reagent kit. Each library was run on three SMRT cells. Sequencing was performed by the Genomics Core of the University Hospital of Leuven. Fastq files were obtained with a minimal requirement of 6 subreads per read of insert.

Zablotskaya A., Van Esch H., Verstrepen K.J., Froyen G, & Vermeesch J.R. (2018). Mapping the landscape of tandem repeat variability by targeted long read single molecule sequencing in familial X-linked intellectual disability. BMC Medical Genomics, 11, 123.

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ChIP-seq Analysis of WOX13 in Roots

Cited 1 time

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ChIP was carried out twice independently as previously reported (Rymen et al., 2019 (link)) with minor modifications. One gram of whole roots was harvested from 14-d-old WOX13gGFP in wox13-2 seedlings and frozen with liquid nitrogen. Samples were ground to a fine powder using a multibeads shocker (MB1200, Yasui Kikai) and the nuclear fraction was isolated after cross-linking for 10 min with 1% formaldehyde (Sigma) under vacuum. Chromatin was sheared at 5°C with a focused ultrasonicator (Covaris) with the following settings: duty cycle 5%, intensity 4, and cycles per burst 200 for 25 min (the first replicate) or duty cycle 10%, intensity 5, and cycles per burst 200 for 15 min (the second replicate). Sheared chromatin was immunoprecipitated using antibodies against GFP (ab290, Abcom). The isolated DNA was quantified with the Qubit dsDNA High Sensitivity Assay kit (Thermo Fisher Scientific) and 1–2 ng of DNA was used to make each ChIP-seq library. Libraries were prepared using the KAPA Hyper Prep Kit for Illumina (KK8502, KAPA Biosystems) and Illumina compatible adaptors (E7335, E7500, E7710, E7730, NEB). Libraries were pooled and 84-bp single-stranded sequences were obtained using Illumina NextSeq500 sequencer.

Ikeuchi M., Iwase A., Ito T., Tanaka H., Favero D.S., Kawamura A., Sakamoto S., Wakazaki M., Tameshige T., Fujii H., Hashimoto N., Suzuki T., Hotta K., Toyooka K., Mitsuda N, & Sugimoto K. (2021). Wound-inducible WUSCHEL-RELATED HOMEOBOX 13 is required for callus growth and organ reconnection. Plant Physiology, 188(1), 425-441.

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Genetic Analysis of 3q29 Deletion

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In patients, peripheral venous blood was analyzed for CGG repeats using the FMR1 with extra‐long and repeated prime polymerase chain reaction. To assess genome‐wide DNA dosage imbalance, array comparative genome hybridization was performed using Agilent 180K Sureprint G3 Human CGH array in the two patients. Subsequently, the presence of the 3q29 deletion was tested in relatives by MRC Holland SALSA MLPA probemix P245 (B1‐0512). Genomic DNA from patients and first‐degree relatives was extracted from peripheral blood using the DNeasy Blood & Tissue Kit (Qiagen). DNA was sheared using a focused‐ultrasonicator (Covaris) and the fragment size of the sheared DNA was assessed by TapeStation (Agilent Technologies). An Agilent SureSelect Target Enrichment System was used to capture the genomic 3q29 region, including intergenic and intragenic regions, excluding repetitive sequences, prior to sample sequencing. The 3q29 region was sequenced by MiSeq, Illumina.

Malt E.A., Juhasz K., Frengen A., Wangensteen T., Emilsen N.M., Hansen B., Agafonov O, & Nilsen H.L. (2019). Neuropsychiatric phenotype in relation to gene variants in the hemizygous allele in 3q29 deletion carriers: A case series. Molecular Genetics & Genomic Medicine, 7(9), e889.

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Sequencing DNA from S. japonicum

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Male and female worms preserved in ethanol of S. japonicum were provided by Lu Dabing from Soochow University (Suzhou, China). DNA was extracted from 28 pooled males and 33 pooled females. The worms were lysed using the Tissue Lyser II kit (QIAGEN) and DNA was isolated using the DNeasy Blood and Tissue Kit (QIAGEN). DNA was then sheared with Covaris Focused-ultrasonicator. Library preparation and sequencing (HiSeq 2500 v4 Illumina, 125 bp paired-end reads) were performed at the Vienna Biocenter Next Generation sequencing facility (Austria). Reads have been deposited at the NCBI Short Reads Archive under accession number SRP135770.

Picard M.A., Cosseau C., Ferré S., Quack T., Grevelding C.G., Couté Y, & Vicoso B. (2018). Evolution of gene dosage on the Z-chromosome of schistosome parasites. eLife, 7, e35684.

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Single-cell transcriptome amplification and sequencing

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Oocytes were incubated with 0.3 mg/ml hyaluronidase (Sigma, St. Louis, MO) to remove the cumulus cells. Zona pellucida was removed from oocytes and embryos prior to lysis. RNA were extracted from single oocytes, 1-cell embryos or whole 2-cell embryos; and cDNA were amplified as described previously with modifications (Tang et al., 2010 (link)). Between 1:10,000–1:60,000 dilution of ERCC RNA Spike-In mix (ThermoFisher Scientific, Hemel Hempstead, UK) was added to lysis buffer to estimate efficiency of amplification (Jiang et al., 2011 (link)). 1:10 dilution of the cDNA was used for RT-qPCR. For relative expression, all genes / TE transcripts were normalised to three housekeeping genes (ARBP, PPIA and GAPDH). For primer sequences see Supplementary file 3. For RNA-seq, cDNA were fragmented to ~200 bp with Focused-ultrasonicator (Covaris, Woburn, MA) and adaptor ligated libraries were generated using NEBNext Ultra DNA library Prep Kit for illumina (New England Labs, Ipswich, MA). Single-end 50 bp sequencing was performed with HiSeq1500 (Illumina, San Diego, CA) to an average depth of 13.5 million reads per sample.

Huang Y., Kim J.K., Do D.V., Lee C., Penfold C.A., Zylicz J.J., Marioni J.C., Hackett J.A, & Surani M.A. (2017). Stella modulates transcriptional and endogenous retrovirus programs during maternal-to-zygotic transition. eLife, 6, e22345.

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ChIP-qPCR Assay for NFATc3

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1 × 10⁷ cells were used per ChIP assay according to a published protocol [21 (link)]. Briefly, cells were crosslinked with 1% paraformaldehyde for 15 min and were quenched with glycine for 5 min at room temperature. Fixed chromatin was sonicated with a Covaris Focused-ultra sonicator and immunoprecipitated with the NFATc3 (Ab6666, ABclonal) antibody. ChIP-qPCR was performed using SYBR-Green PCR Master Mix (Thermo Fisher Scientific) on a ViiA7 PCR machine (Applied Biosystems). Relative enrichments are presented as percentage input. Primer sequences are available on Additional file 1: Figure S6.

Kang T., Ge M., Wang R., Tan Z., Zhang X., Zhu C., Liu H, & Chen S. (2019). Arsenic sulfide induces RAG1-dependent DNA damage for cell killing by inhibiting NFATc3 in gastric cancer cells. Journal of Experimental & Clinical Cancer Research : CR, 38, 487.

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Comprehensive Genomic Profiling for Research

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DNA samples were used for two different assays including whole exome sequencing (WES) and low pass long insert whole genome sequencing (WGS). WES was prioritized if material was limiting. For WES, 50ng-250ng of genomic DNA was fragmented to an average size of 180bp in length using a Covaris focused-ultrasonicator (Covaris). An Illumina sequencing technology compatible whole genome library was created using Kapa Biosystems Hyper Prep Kits. These libraries were then subjected to whole exome target enrichment using Agilent SureSelect V5+UTR hybrid capture kits.
For RNA-sequencing, either 150ng or 500ng of total RNA was used to enrich for poly-adenylated RNA molecules, which were subsequently fragmented to a target size of 180bp by heat fragmentation. Fragmented molecules were then converted to cDNA using random primers with Superscript II (Invitrogen). After second strand synthesis, the resulting molecules were used for library prep using the Illumina TruSeqRNA library kit.

Manojlovic Z., Christofferson A., Liang W.S., Aldrich J., Washington M., Wong S., Rohrer D., Jewell S., Kittles R.A., Derome M., Auclair D., Craig D.W., Keats J, & Carpten J.D. (2017). Comprehensive molecular profiling of 718 Multiple Myelomas reveals significant differences in mutation frequencies between African and European descent cases. PLoS Genetics, 13(11), e1007087.

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