Covaris s2 user manual pdf

A read is counted each time someone views a publication summary such as the title, abstract, and list of authors, clicks on a figure, or views or downloads the fulltext. Rapid wholegenome sequencing of mycobacterium tuberculosis. While bisulfite sequencing has been the gold standard for methylome analysis, this conversion treatment damages dna, resulting in fragmentation, loss and bias. The versatility of afa is now available in a pilot and production scale version, suitable for continuous flow. We are using a library prep kit from nugen for rnaseq. Shearing was completed using the covaris s2 per the user guide for fragment library preparation. Methods are transferable between the s2 system and the automated e210. 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. Genomic hallmarks and structural variation in metastatic. Construction of a mapbased reference genome sequence for.

Dna shearing on covaris m220 with regular pcr tubes. S220 and s220x manual pdf s220 quickstart guide pdf s2 and s1 manual pdf s2x manual pdf software. For 18h wgs, the amount of dna used was optimized, based on experience of varying the input from representative dna samples, and allowed a concentration to be. This operating manual contains important information on proper use and. It contains background information essential to the proper use and care of this equipment. Solid 3 system instrument operation guide pn 4407430b. The aim was to develop a highquality dna library construction method optimized for ngs of ffpe. Covaris s2 instrument or other fragmentation equipment. To load and unload the covaris microtube correctly from the microtube holder, see the covaris s2 user manual. Dna shearing with microtubes s2 or e210 tank should be equipped with a graduated water level label. An operators manual is provided with the equipment. It is a highthroughput, sensitive, and highresolution alternative to the running of agarose gels for the assessment of sizing, quantitation, integrity and purity from dna and rna. Degraded samples were diluted to the suggested input quantity according to manufacturers guidelines innotyper 21 kit input value of 0. Guide pacific biosciences template preparation and.

During treatments, the microtube should be partially immersed in the water to ensure a good acoustic path from the afa transducer. The s220 focusedultrasonicator is a versatile, high power system engineered for preanalytical sample processing with covaris patented adaptive focused acoustics afa. Perkin elmer janus liquid handling system manual this is the document view page. Set the chiller temperature on the covaris s2 to 25c to ensure that higher temperatures during fragmentation can be detrimental. Covaris sseries single tube sample preparation system, model s2 covaris covaris microtube with afa fiber and snap cap covaris pn 520045 nucleasefree 0. Sequencing system library size template kits ion s5 system ion s5 xl system ion genestudio s5 series system 600. This quick guide provides dna shearing protocols when using microtube or minitube and a covaris s2 or. A 26hour system of highly sensitive whole genome sequencing.

Utilizing a spherical acoustic transducer, specifically designed afa tubes, and advanced electronics, afa delivers controlled energy precisely and accurately to sample. Wholegenome sequencing provides comprehensive data on resistance mutations and strain typing for monitoring transmission, but unlike for conventional molecular tests, this has previously been achievable only from cultures of m. Covaris focusedultrasonicators meet your preanalytical sample preparation system needs by delivering highlycontrolled and focused acoustic energy to your samples. The mapbased reference genome sequence of barley cv. My experience so far has been that sometimes it works, and sometimes it doesnt, based on qpcr results of known targets for ets1. This document describes operation of the covaris le220 for shearing cdnagdna. Ama ata aidoo no sweetness here pdf set in s ghana, no sweetness here and other stories is a collection of eleven short stories from ghanaian writer ama ata aidoo.

The circulated water chiller should be supplemented with 20% ethylene glycol. Read this entire manual before attempting to install or operate your asc 2000 ambulatory surgical table. For s2 system equipped with a graduated fill line label, level 12 b. Prostate cancer represents a common and clinically heterogeneous disease entity. Utilizing a spherical acoustic transducer, specifically designed afa tubes, and advanced electronics, afa delivers controlled energy precisely and accurately to sample volumes from 15. Nextgeneration sequencing ngs testing of formalinfixed, paraffinembedded ffpe tissues is widely used in clinical diagnosis. Perkin elmer janus automated liquid handler system tags. There is also a pdf version of this manual on the system computer. All products, chromatin epigenetic research instruments covaris benchtop shearing for ngs and chip m220 focusedultrasonicator is designed for nextgen sequencing and chip applications.

The rapid identification of antimicrobial resistance is essential for effective treatment of highly resistant mycobacterium tuberculosis. The compact size and easeofuse of the m220 focusedultrasonicator make it the ideal chromatin shearing solution for any lab. Ensure that the covaris s2 system is degassed, that no bubbles are present in the. The covaris instructions say to use their special tubes. S220x user manual page 4 warranty when used in accordance with written instruction and under normal operating conditions, the covaris instruments are guaranteed to be free of defects in material and workmanship for one 1 year from the date of original delivery by an authorized representative. User manual covaris dna shearing verification kit for microtube consumables pn 520120 covaris part number. In this document, the instrument generally refers to any of these ele220 series of instruments. Type 0, then press enter for each of the remaining fields. So if you have a spare microtube holder, you can use a round file to make the hole a little larger to fit the tube.

Hi ethan, i am new to chips, but have been trying to optimize our labs chip protocol for use with the covaris s2 instrument. Nextgeneration sequencing using s1 nuclease for poorquality. Covaris provides tools and technologies to improve preanalytical sample preparation, enable novel drug formulations, and manage compounds in the drug discovery process. Enzymatic fragmentation is not recommended as this may result. Fragmentation can be done using a preferred fragmentation device such as a covaris instrument. Place the tube collar at the indicator line of the adaptor. Ensure that the circulated water chiller is set to. Libraries were purified using spri beads beckman coulter. Gigabyte gaep31ds3l manual pdf gaepds3l read user manual online or download in pdf format. Guide pacific biosciences template preparation and sequencing. A single sample was degraded using a covaris s2 sonicator into 75, 100, 150, 200, and 250 bp fragments. S220 and s220x manual pdf s220 quickstart guide pdf. Covaris s2 instrument or other fragmentation equipment pcr strip tubes recommended.

If the tank lacks this label, please contact covaris. While over 160,000 american men are diagnosed with prostate cancer each year, covaris afa technology in a parallel sample processing format for dna fragmentation. Product documentationavailable for download in pdf from the illumina website. Shearing with covaris s220 focusedultrasonicator duke gcb. Chip fragmentation with covaris protocol ethanomics. Agilent 2100 bioanalyzer system the agilent 2100 bioanalyzer system is an established automated electrophoresis tool for sample quality control of biomolecules. Covaris is continuously working to improve our protocols and they are therefore subject to change. Ensure all appropriate personnel understand the contents of this manual. For shearing conditions with the covaris s2 system, see shear the dna with the covaris s2 system on page 14. Documents document view page perkin elmer janus liquid. 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. System is hereby granted limited, nonexclusive rights to use this user guide solely for the purpose of operating the solid. Each strip contains 8 microtube and allows great flexibility when processing samples in varying batch sizes.

Table of contents operator manual 150830442 a word from steris corporation important. Slowly transfer the dna to a microtube loaded into the covaris s2 through the presplit septa, being careful not to introduce any bubbles into the bottom of the tube. Nebnext enzymatic methylseq emseq is a new method for identification of 5mc and 5hmc. Basecalling and alignment were performed on a torrent suite v4. Examination of 20 retrotransposable polymorphic insertion. But if you dont want to alter the holder, pcr tubes still can be used to shear dna but with higher duty factor. Preparation of fragment libraries for nextgeneration. S2 serial, single dna shearing range 100bp3kb 8kb tbd standalone format activex control apis for tecan evo ce marking etl nrtl testing covaris systems shipped 750 units.

Overview of the user manual this manual contains operation and maintenance instructions for the covaris ele220 series focusedultrasonicators e220, e220x, e220r, le220, or le220r. 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. 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. Library preparation guide thermo fisher scientific. Perform required maintenance as described in the solid system 2. Covaris setting m220 s220 s2 e210 dutyfactor% 20 5 10 intensity 5. Fragment library preparation thermo fisher scientific. Part of the kits instructions is to use a covaris s2 to fragment the cdna. The instructions in this document must be strictly and explicitly followed by.