Covaris s2 user manual

This manual contains operation and service instructions for the covaris sseries instruments the s1 and the s2. Allegra x 30r manual, allegra x 30r manual online drug. The aim was to develop a highquality dna library construction method optimized for ngs of ffpe. Documents document view page perkin elmer janus liquid. It contains background information essential to the proper use and care of this equipment. Jun 07, 2016 the gtubes were centrifuged twice at 4200 rpm for 60 s in each direction. To fragment dna to size larger than 5 kb, covaris offers the gtube. This covaris s220 focused ultrasonicator has been tested to ensure all features operate as intended. Protocols are available for shearing dna to sizes of 150 to 1500 base pairs. The sample is placed into a cuvette that is in a nucleasefree environment so the introduction of nucleases is minimized.

Dna shearing on covaris m220 with regular pcr tubes. To shear dna in fragment library preparation, and to declump beads in bead and slide preparation figure 2 covaris s2 system. Covaris s2 focused ultrasonicator for sample processing w chiller pred. Engineered for preanalytical sample processing with covaris patented adaptive focused acoustics.

You can buy with confidence knowing this covaris s220 focused ultrasonicator is ready to go. While bisulfite sequencing has been the gold standard for methylome analysis, this conversion treatment damages dna, resulting in fragmentation, loss and bias. The primary purpose of this protocol is to prepare genomic dna libraries that can then be analyzed by massively parallel nextgeneration sequencing on the applied biosystems solid platform. Chip fragmentation with covaris protocol ethanomics. Ion xpress plus gdna fragment library preparation user guide 3. Also, we hypothesized that shearing efficiency and recovery of frag ments in the right target size range could be. Methods are transferable between the s2 system and the automated. However, the failure of highquality dna library construction, a critical step for ngs, often limits ngs application for ffpe tissues, particularly for old ffpe tissues. Jul 29, 2019 the branched dna bdna assay was performed according to the procedures described in the user manual of quantigeneplex dna assay panomics. Fragment library preparation thermo fisher scientific. Covaris assumes no liability regarding the use of a protocol for applications in which it is not intended or with use of non covaris certified consumables. Unpacking and instructions covaris sseries youtube.

Instrument and software developed for high performance sample preparation using adaptive focused acoustic energy. Covaris focusedultrasonicators meet your preanalytical sample preparation system needs by delivering highlycontrolled and focused acoustic energy to. Zaxis isaac multitester leak tester user manual this is the document view page. Covaris offers preanalytical sample preparation systems such as focusedultrasonicators, proprietary consumables, reagent kits, cryoprep extraction systems, laboratory services, and more. From the final sequencing data, one can verify that all the. Used covaris s220 series adaptive focused sonicator. Set up the covaris s2 or e210 at the appropriate temperature. Fees price includes cost of the cuvette covaris s2. Preparation of fragment libraries for nextgeneration. Extensive sequencing of seven human genomes to characterize. Prostate cancer represents a common and clinically heterogeneous disease entity. Quality control and support instrumentation iowa institute. Ensure that the covaris s2 system is degassed, that no bubbles are present in the.

Documents document view page zaxis isaac multitester leak. Covaris inc company profile and news bloomberg markets. Covaris focusedultrasonicators are engineered to meet your sample preparation needs by delivering highlycontrolled and focused acoustic energy to your samples. Exonenriched libraries reveal large genic differences. A highquality genome assembly of the north american song. It is required to provide a covaris shearing protocol and desired fragment length bp when submitting samples.

We applied this approach to an rna mixture derived from three diverse cultured bacterial species and to rna isolated from clinical stool samples. Genomic hallmarks and structural variation in metastatic. Registered names and trademarks used in this document, even when not specifically marked as such, are not to be considered unprotected by law. System is hereby granted limited, nonexclusive rights to use this user guide. This protocol can be adapted to nextgeneration sequencing workflows. Solid 3 system instrument operation guide pn 4407430b. Shearing with covaris s220 focusedultrasonicator duke gcb. Documents document view page waters quattroflow s.

While over 160,000 american men are diagnosed with prostate cancer each year, covaris sseries user manual 2 trademarks patented or patent pending are and registered or registrationpending are trademarks of covaris. A minor but significant fraction of samples subjected to nextgeneration sequencing methods are either mixedup or crosscontaminated. For every chemical, read the sds and follow the handling instructions. Covaris s2 focused ultrasonicator for sample processing w.

We are using a library prep kit from nugen for rnaseq. Preface samplepreparation equipment the samplepreparation equipment includes. Covaris system s2, e210 or other method for dna fragmentation. Covaris is continuously working to improve our protocols and they are therefore subject to change. Shearing was completed using the covaris s2 per the user guide for fragment library preparation. S220 is about 2x more expensive, but is it really more useful for chromatin shearing, for example. Utilizing a spherical acoustic transducer, specifically designed afa tubes, and advanced electronics, afa delivers controlled energy precisely and accurately to sample volumes from 15. The workflow described in the nebnext enzymatic methylseq kit is userfriendly and enables methylation detection from inputs ranging between 10 ng200 ng. Nextgeneration sequencing ngs testing of formalinfixed, paraffinembedded ffpe tissues is widely used in clinical diagnosis. Covaris s2 or e210 system and appropriate tubes various microplate centrifuge various thermocycler biorad laboratories mj research dna engine ptc200, or equivalent microamp clear adhesive plate seals applied biosystems 4306311 labchip gx or agilent bioanalyzer with appropriate chips and reagents various. Beckman allegra 25r with ts used laboratory centrifuges, heraeus, mse, hettich, beckman allegra 25r refrigerated bench top centrifuge, max speed 14,rpm with angled rotor and rpm with swingout rotor, induction motor, motorised lid locking, including 1 x microplate rotor s2 x microplate carriers. Benchtop, high intensity acoustic transducer, temperature monitoring device, circulation pump, water bath with safety enclosure. Briefly, the homogenate dna was sheared by the covaris s2 covaris, woburn, ma with the following settings.

At covaris, supporting our customers is a top priority, but the current covid19 situation requires a firm commitment to the health and safety of our employees, customers, and communities that. Efficient and robust rnaseq process for cultured bacteria. Apr 01, 2020 the song sparrow, melospiza melodia, is one of the most widely distributed species of songbirds found in north america. This kit allows users to routinely verify the performance of their covaris. For s2 system equipped with a graduated fill line label, level 12 b.

Mseries user manual me220 user manual ml230 user manual sseries s1 and s2 user. Each strip contains 8 microtube and allows great flexibility when processing samples in varying batch sizes. Nextgeneration sequencing using s1 nuclease for poorquality. Covaris instruments, is one of the most commonly used to fragment gdna prior to library construction. To load and unload the covaris microtube correctly from the microtube holder, see the covaris s2 user manual. Afa does not require soundproof boxes, hearing protectors, or other unusual precautions for their operation. Hi ethan, i am new to chips, but have been trying to optimize our labs chip protocol for use with the covaris s2 instrument. If the tank lacks this label, please contact covaris. Hi all, so i have been working for some time to optimise my chromatin shearing for chip using a covaris s2. These events can lead to false or inconclusive results. Fragment gdna with the covaris s2 and s220 systems. My experience so far has been that sometimes it works, and sometimes it doesnt, based on qpcr results of known targets for ets1. An operators manual is provided with the equipment. Part of the kits instructions is to use a covaris s2 to fragment the cdna.

We offer ultrasonicator instruments and software capable of meeting your needs. Optimization of covaris settings for shearing bacterial. The covaris system uses adaptive focused acoustics afa to shear samples. Nebnext enzymatic methylseq emseq is a new method for identification of 5mc and 5hmc. Ion xpress plus and ion plus library preparation for the ab.

The circulated water chiller should be supplemented with 20% ethylene glycol. Set the chiller temperature on the covaris s2 to 25c to ensure that higher temperatures during fragmentation can be detrimental. Dna fragmented with the bioruptor system or the covaris system and sizeselected with the pippin prep instrument 94 contents 6 ion xpress. This species pronounced morphological and behavioral diversity across populations makes it a favorable candidate in several areas of biomedical research. Covaris setting m220 s220 s2 e210 dutyfactor% 20 5 10 intensity 5. Cp02 automated cryoprep system user manual cp01 cryoprep manual. Waters quattroflow s 4piston diaphragm pump user manual this is the document view page. Using a covaris gtube shearing device 5 kb insert sizes the most uptodate guidance on how to use the gtube device, along with recommended centrifuges and centrifugation speeds, can be found in the gtube device user manual available for download from the covaris web site. Frequent genetic aberrations in the cell cycle related genes. From what i gathered prior to starting, the covaris is a better alternative to tip sonicators as it keeps the sample nice and cool during sonication, is supposedly less harsh on the chromatin, and also minimises sample crosscontamination as no direct contact is made with the sample. Perkin elmer janus liquid handling system manual this is the document view page. Guide pacific biosciences template preparation and sequencing. Dna shearing with microtubes s2 or e210 tank should be equipped with a graduated water level label. During treatments, the microtube should be partially immersed in the water to ensure a good acoustic path from the afa transducer.

The covaris s2 shears nucleic acids into suitably sized fragments for ngs library prep using focused acoustic energy. It has been used in a wide range of behavioral and ecological studies. For shearing conditions with the covaris s2 system. Essentially, two parameters are to be optimized for a given type of sample. Emseq converted dna is more intact than bisulfiteconverted dna, resulting in libraries with longer sequencing reads, reduced gc bias and more even genome coverage. In order to sonicate a sample all interlocks, electronics, degassing pump and ultrasonic generator must function properly.