Search results for: library prep
What is Volume Electron Microscopy and Should You Use it?
…with your sample prep, as it largely dictates whether your vEM imaging project will succeed or fail. We have an excellent guide to EM sample prep, and many of the…
Read More7 Top Tips to Make the Most of Your Flow Cytometry Training
…to advise you on sample prep and provide tips for sample-specific instrument setup. The type of experiment you will perform. Will it be immunophenotyping or a functional assay such as…
Read More5 Tips on Vector Preparation for Gene Cloning
…prep – you will likely regret it later. 2. Pay Attention to the Digest The digest looks easy on paper, but don’t underestimate the importance of good planning and execution…
Read MoreBattle of the Methods: Whole Transcriptome Versus mRNA-seq
…RNA Library Prep Kits for IlluminaTM systems that add helper adaptors directly onto the RNA before cDNA is generated later on in the workflow. Fresh or Frozen Tissue Versus FFPE…
Read MoreWhy DNA Size Selection Matters in NGS Pipelines
Of all the sample prep steps necessary for next generation sequencing, DNA size selection may have the greatest impact on quality of results. After all, ineffective sizing can waste sequencing…
Read MoreChoosing a Scripting Language for Next Generation Sequencing: Python, Perl, and More
…difficult to read and understand someone else’s scripts. One benefit of Perl’s staying power is that the BioPerl library is more mature and larger than the BioPython library. Chances are…
Read MoreDNA Extraction from FFPE Tissues for NextGen Sequencing
…nucleic acid crosslinking caused by formalin fixation without causing further DNA damage. Beyond that, extracted DNA requires controlled shearing into manageable fragments for NGS library preparation. DNA Extraction and Shearing…
Read MoreProbability Theory and Molecular Barcodes
…As an example, this approach enables parallel sequencing of different samples through the labeling of each library with a distinguishing barcode, or index (e.g. Illumina indexing). The procedure is straightforward:…
Read MoreZymo Research’s Mix & Go! Competent Cells: They’re Shocking… But Only to You!
…yield making them ideal for general cloning and library construction. TG1 and C600 strains are recombination competent. HB101 cells are excellent for library construction. 4. Choose your format: single aliquots,…
Read MoreBest Practices for DNA Shearing for NGS
Construction of high-quality sequencing libraries is pivotal to successful NGS, and DNA quality is one of the most critical aspects of library preparation. As this Nature Methods paper illustrates, DNA…
Read MoreNext Generation Sequencing: The Three Main Technologies
…(such as Helicos) and new systems are being developed for the next big leap forward. At the same time, there has also been significant progress in sample-prep technology for Whole…
Read MoreSAGE Part 2: LongSAGE, RL-SAGE and SuperSAGE
…take 5 ?g of mRNA to create a library of hundreds of cDNA tags. In comparison, LongSAGE published in 2002 in Nature Biotech, could use 20 ?g of mRNA to…
Read MoreHow to Culture Primary Human Bronchial Epithelial Cells
…to harvest sufficient HBECs. The prep – Decontamination As soon as you remove brushes from the patient, incubate the brushes immediately in sterile medium. You can store the brushes (with…
Read MoreTroubleshooting DNA Ligation Problems
…prep for our ligation and controls, the number of colonies formed will be dependent on the amount covalently-closed DNA we have in each reaction (i.e. how successful the ligation has…
Read MoreTroubleshooting RNA Isolation
…of tissue so make sure you are using a scale accurate to the weight you need or you may see variation from prep to prep as well as other problems…
Read MoreIf You Use Plasmid Midi and Maxi preps, Your Life is About to Get Much Easier
…history in removing the pain from nucleic acid prep procedures, with innovations like pioneering the first zero retention micro-elution spin column. But their latest offering – ZymoPURE™ MidiPrep and MaxiPrep…
Read MoreUnder Pressure: Tips for Keeping Your HPLC Up and Running Properly
…to remove any particulate matter that might clog the instrument. Just be sure that your filter is compatible with the solvent you are using! 2. Sample Prep Will Make or…
Read MoreThe 31 Flavors of Drosophila Electrophysiology Recording Solutions
…the case of myosin, compete for calcium binding sites. But magnesium has a longer dwelling period at the binding site, which can cause your prep to lose some movement. I…
Read MoreHow to Set up Your Elution Experiment
…solid phase, which can be a silica gel in the case of mini-prep columns, but usually beads that can be covalently linked to antibodies or other ligand molecules. “Solid phase”…
Read MoreHow to Use a Eukaryotic System for Protein Expression & Purification
…stage to identify recombinant constructs. Recombinant bacmid DNA is then isolated from the transformed E. coli using PureLinkTM HiPure Mini-prep kit. The size of the recombinant bacmid is large and…
Read MoreHow to Perform RNA Quality Control in the Lab: 3 Key Considerations
…it to set. Mix a small volume of your RNA prep with a loading dye. Add the RNA prep and loading dye into a well. Add your running buffer and…
Read MoreIf You Use Plasmid Midi and Maxi Preps, Your Life is About to Get Much Easier
…history in removing the pain from nucleic acid prep procedures, with innovations like pioneering the first zero retention micro-elution spin column. But their latest offering – ZymoPURE™ MidiPrep and MaxiPrep…
Read MoreSome Sanger Sequencing Tips and Tricks
…of plasmid prep: You don’t need to plasmid prep your clones for Sanger sequencing. After picking clones for culture, simply swirl your cocktail and stick into a PCR master mix…
Read MoreThree Insights for Choosing the Best DNA Size Selection Method for Your Project
…team evaluated Novex TBE PAGE gels, the Pippin Prep automated DNA sizing platform from Sage Science, and AMPure XP beads, noting that their goal was to assess strengths and weaknesses…
Read MoreIgnore The Ticking Bomb At Your Peril: RNA-Seq Normalization- A Lurking Problem And It’s Solution.
You have spent days, if not weeks, at the bench setting up the treatment and control samples for that crucial experiment. You submitted your cDNA library for sequencing and after…
Read MoreWhy Is It Important To Run Your NGS Gels Consistently?
…low-input samples. Many NGS library preparation protocols use agarose gels for size selection of genomic DNA, RNA or final libraries. Gel electrophoresis is a simple size selection technique and is…
Read MoreUsing PubCrawler: How to Speed Up Your Literature Searches by Crawling
…can also be a significant source of stress. In Search of a Library Assistant When I was a graduate student, I would diligently search PubMed for the newest articles published…
Read MoreNail Your Unmixing for Full Spectrum Flow Cytometry: 7 Top Tips
…record them into a reference library for reuse. DO: validate how long the reference library controls can be reused. The rule of thumb is one month, but you should validate….
Read MoreLet’s Get Melting
…all known drug-resistance genes/mutations associated with the microbe of interest. Melt curves obtained from patient samples are then compared to the reference library. Library preparation is typically carried out by…
Read MoreHow to Get Organized With Reference Managers for Science—EndNote
…write—just remember to have the EndNote library you are using open in the background. With this feature, there’s no need for you to switch between programs or documents. This is…
Read MoreAn Easy Way to Start Using R in Your Research: Making Pretty Plots With ggplot
…you need to add the package to the ’library’ of functions that R knows how to use. You do this with the function library(): library(ggplot2) (In these articles, commands to…
Read MoreOut With the Old: New PubMed Search Tips
…US National Library of Medicine has a great webinar with downloadable slides if you want to learn more of access materials for training. [8] Hopefully the updated design and additional…
Read MoreWhy Is It Important To Run Your NGS Gels Consistently?
…gel is a critical step that must be carried out very carefully. Many of the NGS library preparation protocols use agarose gels for size-selection of genomic DNA, RNA or final…
Read MoreTeach Yourself Python: A Guide for Biologists
…and data analysis and visualization. Biopython is an open-source library made for computation in bioinformatics. PyMed is another library that can help researchers make consistent and readable batch search queries…
Read MoreBreaking Down the Assembly of Nucleic Acid Sequences
…you need to prep it for sequencing. You might need to shear the nucleic acid to obtain a library with a specified insert size, and then add adapters to the…
Read MoreTips on Restriction Digests: Designing a Restriction Screen
…functional). a restriction site has been added or removed. the vector prep is dirty and may contain contaminates that inhibit the digestion reaction. Reperform the prep (e.g. miniprep) if you…
Read MoreThere’s No Need To Be Paranoid About RNA Purification
…and pipettes, and floating in the air, waiting for the chance to creep into your prep, shred your RNA into nucleotides, and ruin a day’s work. Well, not really. It’s…
Read MoreTop Tips to Keeping Your Logbook in Shipshape
…and then go to your logbook to see more details as necessary. You can also use this to keep tabs on which culture/prep you have used and which is therefore…
Read MoreDigital PCR or Quantitative Real-Time PCR: Which Method Is Best for Your Quantitative PCR Application?
…and Digital PCR (dPCR). Which one is right for your application? Both methods have good quantification, sensitivity and specificity for most applications. They are compatible with the same sample prep…
Read MoreA DIY Method for Isolating Yeast Genomic DNA
…DIY prep for a while. Why Use a DIY Method for DNA Isolation? Unlike with kits, there are no propriety reagents in a DIY protocol. You know what exactly is…
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