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Sonicator

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The Sonicator is a laboratory instrument used to disrupt and homogenize samples through the application of ultrasonic waves. It is designed to break down cellular, tissue, or other solid materials into smaller fragments or a uniform suspension.

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Lab products found in correlation

Truseq nano dna lt kit, by Illumina (2 mentions) Hiseq 2000, by Illumina (1 mentions) Nextflex dna sequencing kit, by PSC Biotech (1 mentions) Truseq nano dna kit, by Illumina (1 mentions) Cell lysis solution, by Qiagen (1 mentions) Hiseq 4000 machine, by Illumina (1 mentions) Novaseq 6000, by Illumina (1 mentions) Bioanalyzer, by Agilent Technologies (1 mentions) Kapa hyper prep kit, by Illumina (1 mentions) Hiseq 2500, by Illumina (1 mentions) Hoescht dye, by Merck Group (1 mentions) Qiasymphony dna extractor, by Qiagen (1 mentions)

Spelling variants of this product

S2 sonicator (6 citations)

6 protocols using sonicator

1

Illumina and PacBio Sequencing of Metagenomic DNA

Cited 2 times
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The DNA was sheared in a Covaris sonicator and Illumina paired-end libraries with insert sizes of 170 bp, 210 bp, and 430 bp, were constructed using the NEXTflex DNA Sequencing kit (Bioo Scientific). Libraries were sequenced with an Illumina HiSeq 2000 system. 2 x 100 bp paired-end reads in FASTQ format were filtered using custom Python scripts to remove low quality reads (link)] was also used to error correct the reads. Additional filtering was performed to remove bacterial sequences. Most of these sequences were E. coli sequences, which accounted for 3% of total sequences. Additional bacterial contamination from genera Pseudomonas and Sphingonomas was detected based on the coverage distribution of the genome, and filtered out (<1%).
PacBio library preparation and sequencing were performed according to the manufacturer’s instructions (Pacific Biosciences), and as described in reference [101 (link)]. Libraries were sequenced on the Pacific Biosciences (PacBio) RS system of the Icahn School of Medicine at Mount Sinai, NY, using 8 SMRT® Cells. To improve the quality of the PacBio reads, we processed them with the PacBioToCA tool that mapped the shorter high quality Illumina reads to perform error correction of the longer PacBio reads [90 (link)]. The average read length after correction was 2.5 Kb.
Fradin H., Kiontke K., Zegar C., Gutwein M., Lucas J., Kovtun M., Corcoran D.L., Baugh L.R., Fitch D.H., Piano F, & Gunsalus K.C. (2017). Genome architecture and evolution of a unichromosomal asexual nematode. Current biology : CB, 27(19), 2928-2939.e6.
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2

Comparative Genomics of Listeria Species

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Chromosomal DNA was prepared from 2 mL cultures of L. seeligeri RR4 and L. ivanovii RR3 via lysozyme treatment and phenol-chloroform extraction and ethanol precipitation. DNA samples were sheared using a Covaris sonicator, prepared for deep sequencing using the Illumina TruSeq Nano DNA LT kit, and paired-end 2×300 bp sequencing was conducted on the MiSeq platform. Reads were quality-trimmed using Sickle (https://github.com/najoshi/sickle), and assembled into contigs using Abyss (https://github.com/bcgsc/abyss). Finally, contigs were mapped to reference L. seeligeri and L. ivanovii genomes using Medusa (http://combo.dbe.unifi.it/medusa). Automated genome annotation was performed using BaSys (https://www.basys.ca). Raw reads as well as assembled genomes have been deposited to GenBank under BioProject accession number PRJNA512236.
Meeske A.J., Nakandakari-Higa S, & Marraffini L.A. (2019). Cas13-induced cellular dormancy prevents the rise of CRISPR-resistant bacteriophage. Nature, 570(7760), 241-245.
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3

Genomic DNA Extraction and Sequencing

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Frozen flies of the desired genotypes were pooled, pulverized with sterilized mortar and pestle that are chilled in liquid nitrogen, and then transferred to 50-ml falcon tubes. After adding 15 ml of Cell Lysis Solution from Qiagen (Catalog No.158908), samples were incubated at 65 °C for 4 h and vigorously shaken every hour. In total, 75 μl of ProteinaseK (Catalog No. 19131) was then added and incubated at 55 °C overnight; 200 μl of EtOH was added into 400 μl of the sample then passed through the columns from the DNeasy kit (Catalog No. 69506). The columns were then processed in accordance with the kit protocol. DNA for parental lines were extracted from five females using the DNeasy kit. The resulting DNA was fragmented to 550 bp using the Covaris sonicator and libraries were made with the Illumina Truseq DNA Nano kit. Library quality was determined with the Bioanalyzer at the Functional Genomics Laboratory at UC Berkeley and samples were pair-end sequenced using the Illumina HiSeq 4000 machine at the Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley. Coverage of each cross can be found in supplementary table 1, Supplementary Material online.
Wei K.H., Mantha A, & Bachtrog D. (2020). The Theory and Applications of Measuring Broad-Range and Chromosome-Wide Recombination Rate from Allele Frequency Decay around a Selected Locus. Molecular Biology and Evolution, 37(12), 3654-3671.
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4

Comparative Genomics of Listeria Species

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Chromosomal DNA was prepared from 2 mL cultures of L. seeligeri RR4 and L. ivanovii RR3 via lysozyme treatment and phenol-chloroform extraction and ethanol precipitation. DNA samples were sheared using a Covaris sonicator, prepared for deep sequencing using the Illumina TruSeq Nano DNA LT kit, and paired-end 2×300 bp sequencing was conducted on the MiSeq platform. Reads were quality-trimmed using Sickle (https://github.com/najoshi/sickle), and assembled into contigs using Abyss (https://github.com/bcgsc/abyss). Finally, contigs were mapped to reference L. seeligeri and L. ivanovii genomes using Medusa (http://combo.dbe.unifi.it/medusa). Automated genome annotation was performed using BaSys (https://www.basys.ca). Raw reads as well as assembled genomes have been deposited to GenBank under BioProject accession number PRJNA512236.
Meeske A.J., Nakandakari-Higa S, & Marraffini L.A. (2019). Cas13-induced cellular dormancy prevents the rise of CRISPR-resistant bacteriophage. Nature, 570(7760), 241-245.
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5

Illumina Library Preparation from DNA

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Amplified DNA was fragmented using a Covaris sonicator to achieve an average size of 400bp, and Illumina PCR-free libraries were prepared from ~200–400ng DNA using the KAPA Hyper prep kit and unique dual-indexed adapters (5μl of a 15μm stock) according to the supplier’s protocol (Roche). The library concentration and size distribution were assessed on a Bioanalyzer (Agilent Technologies). Barcoded libraries were pooled at equimolar concentrations and sequenced on a NovaSeq6000 instrument (Illumina, San Diego, CA, United States) to generate 150-bp paired-end reads.
Grosso V., Marcolungo L., Maestri S., Alfano M., Lavezzari D., Iadarola B., Salviati A., Mariotti B., Botta A., D’Apice M.R., Novelli G., Delledonne M, & Rossato M. (2021). Characterization of FMR1 Repeat Expansion and Intragenic Variants by Indirect Sequence Capture. Frontiers in Genetics, 12, 743230.
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6

DNA Extraction from Various Biological Samples

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DNA from 1.0-ml EDTA blood vacutainer tubes was extracted (DSP Blood Midi Kit with QIA Symphony DNA extractor, Qiagen). A custom 1.0-ml EDTA blood protocol was run on the QIA Symphony with DNA eluted in 200 μl TE (Qiagen, without azide). DNA from bone marrow aspirates, fresh and frozen tumor tissues, and blood (volume of <1.5 ml or with low white blood cell count) was extracted with the QIAamp Micro silica-based membrane column kit (Qiagen). Specimen input of 1–8 mg of tumor tissue, 50 μl of bone marrow aspirate or 100 μl of blood was extracted on a single QIAamp microcolumn and eluted in 20 μl TE. DNA was extracted from FFPE tissue using the QIAamp DNA FFPE tissue kit (FFPE tumors were included for participants 92, 170, 200, 209, 228 (2 samples), 269, 273 (2 samples), 299, 306, 358, 362, 370, 375, 376, 377, 384 and 400). DNA was quantitated with a Biomek FLX800 fluorimeter using 2 μl DNA, diluted in 198 μl assay B solution containing Hoescht dye (Sigma). A standard curve of 25–450 ng DNA was prepared using commercial genomic DNA (Sigma), and patient DNA was quantified using this curve. Using the SureSelectXT kit, samples were processed using 200 ng DNA. After shearing the DNA (Covaris sonicator), Illumina HiSeq 2500-compatible libraries were generated. Samples were pooled in multiples of six.
Villani A., Davidson S., Kanwar N., Lo W.W., Li Y., Cohen-Gogo S., Fuligni F., Edward L.M., Light N., Layeghifard M., Harripaul R., Waldman L., Gallinger B., Comitani F., Brunga L., Hayes R., Anderson N.D., Ramani A.K., Yuki K.E., Blay S., Johnstone B., Inglese C., Hammad R., Goudie C., Shuen A., Wasserman J.D., Venier R.E., Eliou M., Lorenti M., Ryan C.A., Braga M., Gloven-Brown M., Han J., Montero M., Spatare F., Whitlock J.A., Scherer S.W., Chun K., Somerville M.J., Hawkins C., Abdelhaleem M., Ramaswamy V., Somers G.R., Kyriakopoulou L., Hitzler J., Shago M., Morgenstern D.A., Tabori U., Meyn S., Irwin M.S., Malkin D, & Shlien A. (2022). The clinical utility of integrative genomics in childhood cancer extends beyond targetable mutations. Nature Cancer, 4(2), 203-221.
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