Search results for: library prep
An Introduction to RNA-seq
…library prep which includes end-repair, adapter ligation and PCR amplification to give you a library ready for sequencing. Why Bother With Strand Information? There has been a lot of discussion…
Read More Solid Phase Reversible Immobilization: How To Get A Bead On The Clean-up Of Your NGS Libraries
…concerned with reproducible library preps, gel purification after adaptor ligation is the step that requires the most attention to detail (see James Hadfield’s excellent instructions of what you need to…
Read MoreAAV Production Part II: Virus Purification
…Sigma-Aldrich sells iodixanol as ‘Optiprep’. See the paper ‘AAV-mediated gene targeting methods for human cells’ for the different iodixanol solution recipes. First, prepare PBS-MK and NaCl/PBS-MK buffers. PBS-MK buffer: Dissolve…
Read More Useful Tips to Keep on Top of New Literature
…on what is already in your library and what you’ve recently read. These recommendations are available directly through ReadCube making it simple to add them straight to your library. CiteULike…
Read More The Cell: An Image Library-CCDB – Tutorial Part 4
…for greater ease of collaboration with other groups using the same ontologies, are also in place to prepare The Cell for semantic web searching. To use these ontological terms, we…
Read More RNAseq Library Preparation: From Cells to cDNA
…(next generation) sequencing of cDNA 5) in silico sequence alignment1, 2. This article is about the two first stages of making an RNAseq library (steps 1- 3). Starting Material Preparation…
Read More Proteomics and Good Mass Spectrometry Data
…if not removed prior to sample prep. Whew! That was a lot. Maybe most importantly, you should have everything set up for sample prep day. And plan your experiments carefully…
Read MoreNanopore Sequencing: An Update
…and I got an update from multiple users at the UK Genome Science conference. Library prep methods are pretty standard: DNA, frag, end repair, A-tail, adapter ligation. Sequencing accuracy is…
Read More NGS-Based HLA Typing Delivers More Comprehensive Information
…size selection is an essential step in library preparation for consistently generating reliable results. HLA Typing Using NGS Requires DNA Size Selection for Library Preparation In the protocol released in…
Read More Next Generation Sequencing: The Three Main Technologies
…(but without the cloning part!). The different NGS platforms have slightly different library preparation methods, the major difference being ‘cluster generation’ for Illumina, and ‘emulsion PCR’ for Roche and Life…
Read MoreStudying the Epigenome by Next Generation Sequencing
…Thus, all that will remain is a library of fragments of methylated DNA, ready to be sequenced. Methyl-CpG binding domain protein sequencing (MBD-seq) The MBD family of proteins contains a…
Read More Battle of the Bargains: A Comparison Between Genome Compiler and ApE
…your own files and those provided in the Genome Compiler library. ApE does have an inventory of enzymes to choose from, but no sequence library, and finding the enzyme selector…
Read More Six Important Factors for Successful Reverse Transcription
…gDNA, such as DNase treatments during an RNA Prep or DNase treatments after a prep (such as the Turbo DNA-Free Kit by Ambion). However, a better way to get around…
Read More 5 Tips on Vector Preparation for Gene Cloning
…Discard and repeat the digest. It may be necessary to re-prepare the vector as a contaminants in the vector prep could inhibit the digest. 3. Prevent Re-ligation If the cut…
Read More Why 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 More Breaking Down the Assembly of Nucleic Acid Sequences
…nucleic acid equally. This can be difficult due to the heterogeneity of the sample. Once extracted and before library preparation, quantify the nucleic acid and assess the quality. Pro tip:…
Read More Battle 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 More Choosing 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 More DNA 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 More Probability Theory and Molecular Barcodes
…during the library preparation, ligate the fragments from each sample to a short, characteristic barcode so that they all share a common sequence. Then sort the reads according to their…
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