Search results for: ChIP seq
An Introduction To ChIP-seq
…more commonly ChIP is interrogated with microarrays (ChIP-chip) or next-generation sequencing (ChIP–seq). How does ChIP-chip work? ChIP-on-chip, or ChIP-chip, combines chromatin immunoprecipitation with microarray (chip) analysis. In 2001, Jason Lieb…
Read MoreVariations on the ChIP-seq Theme and Challenges of Befriending Large Datasets
…Assay for Transposase-Accessible Chromatin-seq (ATAC-seq), and Formaldehyde-assisted Isolation of Regulatory Elelments–seq (FAIRE-seq) reveal regions of open chromatin, not associated with any protein In DNase-seq, the DNase I endonuclease fragments the…
Read MoreExplained: Sensor Chips for Surface Plasmon Resonance and Other Applications
…to use for an experiment, and the latest advances in chip design and production. The Sensor Chip Surface A typical SPR biosensor chip is a glass chip coated with a…
Read MoreFrom ChIP-seq to MeDIP: A Glossary of Different NGS techniques
…similar to ChIP–seq. MeDIP-seq employs antibodies against DNA methylation, while MAP-seq uses a naturally occurring protein with a comparable affinity for DNA methylation. The resolution of both these methods is…
Read MoreAn Introduction to RNA-seq
…major methods being used today. Why Is RNA-Seq “Better” Than Microarrays? There are several advantages RNA-seq has over microarrays: With RNA-seq you can interrogate more than just differential gene expression….
Read MoreRNA-seq: The Challenges to Diving Right In
…RNA and you’re ready to do some RNA-seq. Right? Not quite. You have a lot more to figure out first. This is perhaps the most challenging aspect of RNA-seq. Since…
Read More3′ mRNA-Seq is Transforming Gene Expression Analysis
…chemistry. 3? mRNA-Seq: A Simpler Alternative for NGS Expression Profiling 3? mRNA-Seq also offers the ability to study expression levels of many genes simultaneously and without prior knowledge of the…
Read MoreGenomic Analysis of Single Cells: The Benefits of Being Single
…(RNA-seq), translation (Ribo-seq) genomes (DNA-seq), interactions of proteins and DNA (ChIP–Seq) or to study epigenetic features such as methylation (whole genome bilsulfite sequencing) there are a range of techniques available…
Read MoreGenerating RNA-seq Libraries from RNA
…Disadvantages of Using RNA-seq RNA-seq typically begins with fragmentation followed by generation of cDNA. Unfortunately, this often came with a slew of complications. For instance, as scientists we know that…
Read MoreChIP-seq Workflows Run Best with Automated DNA Size Selection
Chromatin immunoprecipitation sequencing, better known as ChIP–seq, is a massively parallel approach for understanding the interactions between proteins and DNA. This is especially important for determining the activity of transcription…
Read MoreThe Next Big Thing: Alternative Polyadenylation
…fragments containing poly(A), and use an NGS-platform for sequencing; these approaches are known as 3’-enriched RNA-seq. 3’-enriched RNA-seq approaches have advantages over RNA-seq in studying polyadenylation sites and quantifying different…
Read MoreDon’t Get Lost in RNA-seq Translation: RNA Sequencing the NGS Way
…how RNA-seq shows us the important differences between coding mRNA (Poly-A) versus total RNA in a sample, how to properly align NGS RNA data, and comparisons between RNA-seq and microarrays….
Read MoreUse ddRAD-seq to Study Non-Model Organisms
…made modifications to the method to tackle different types of studies. These include; EpiRad-seq (epigenetic data), HyRAD-seq (degraded samples), and SLAF-seq (large populations). Further Reading Sage Science. Hoekstra Case Study….
Read MoreAnalyzing RNA-Seq Data
…faster to come across. Key Metrics in RNA-Seq A number of key data points have been found to be valuable for interpreting RNA-seq results. These include: Total, mapped and transcript-associated…
Read MoreIgnore The Ticking Bomb At Your Peril: RNA-Seq Normalization- A Lurking Problem And It’s Solution.
…your RNA-seq data! Loven J., et al. (2012) Revisiting global gene expression analysis. Cell, 2012. 151(3):476-482. Jiang L., et al. (2011) Synthetic spike-in standards for RNA-seq experiments. Genome Res, 21(9):1543-1551….
Read MoreExamining Cell Interactions with Surface Plasmon Resonance (SPR) and Identifying Epitopes using SPR-Mass Spectrometry (MS)
…research and diagnostics. SPR-MS Two Ways: On-Chip and Off-Chip SPR is coupled to MS using one of two configurations. One setup involves eluting the captured ligand from the SPR chip…
Read More7 Tips for Preparing Chromatin for ChIP from Tissues (Rather than Cells)
…aimed at performing ChIP on cultured cells. In my experience, this is not at all the same as performing ChIP on chunks of tissue. Stay with me for Top Tips!…
Read MoreAll in the Chip: Ion Torrent Sequencers
…sequencer work? Ion Torrent sequencing is based on a unique technology. Instead of optically reading dye-labeled nucleotides, Ion Torrent detects electrical signals on a semiconductor chip. For the Ion Torrent…
Read MoreBattle of the Methods: Whole Transcriptome Versus mRNA-seq
Maybe you want to examine the entire transcriptome or maybe you want to investigate changes in expression from your favorite gene. You could do whole transcriptome sequencing or mRNA-seq. But…
Read MoreNGS Quality Control in RNA Sequencing- Some Free Tools
RNA sequencing (‘RNA-seq’) has become one of the most widely used applications for Next-Generation Sequencing. RNA-seq can provide gene expression data more cheaply than microarray, at greater sensitivity, and without…
Read MoreNext Generation Sequencing: The Three Main Technologies
…few commonly accepted defaults (e.g. Single-end 36 bp for ChIP–seq and Paired-end 100 bp for Cancer genomes). ChIP–seq studies require high numbers of short-reads so these are generated on short…
Read MoreA Crash Course in Epigenetics Part 2: The toolbox of the epigeneticist
…Comparing different conditions and amplicons gives insight into chromatin configuration under certain circumstances. ChIP – the sequel ChIP is not only a valuable tool for studying histone modifications (or the…
Read MoreStudying the Epigenome by Next Generation Sequencing
…principle allow for a quick and effective genome-wide valuation of methylation but do not give info on individual CpG dinucleotides. Methylated DNA immunoprecipitation sequencing (MeDIP-seq) MeDIP-seq relies on immunoprecipitation to…
Read MoreiPOND, Part 2: Why Should You Go Fishing with iPOND?
…using EdU labeling of the DNA. Round 2: iPOND vs. ChIP Chromatin immunoprecipitation (ChIP) is another technique often used to investigate proteins associated with DNA. ChIP is similar to iPOND…
Read MoreTop 10 Tips for NGS Library Preparation
…and ChIP–seq. 3. Take Care with Your SPRI (or Similar) Beads Dispense your beads into single use aliquots for storage at 4oC, let them get to room temperature then vortex…
Read MoreA Beginner’s Guide to Single-Cell RNA Sequencing
…performed on tissue samples or cell populations. Biological differences between cells can be mistaken for technical noise or obscured by averaging. However, single-cell RNA sequencing (scRNA-seq) goes a step further….
Read MoreHow To Analyze Your Single Nucleotide Polymorphism (SNP) Chip Data
So, you’re sitting there with your list of significant SNPs, thinking, “what do I do now”? Hopefully this article can point you in the right direction! So far, you will…
Read MoreAdventures in Genomics: Single-Cell Sequencing in Cancer
…al. Accounting for technical noise in single-cell RNA-seq experiments. Nature Methods 2013 Navin N, Krasnitz A, Rodgers L, et al. Inferring tumor progression from genomic heterogeneity. Genome Res 2010 Navin…
Read MoreHow Can A Single Mutation Affect Splicing Regulation?
…RNA-sequencing (RNA-seq) uses adapter-tagged libraries of short cDNAs prepared from fragmented total RNA, and generates tens to hundreds of millions of short sequence reads in just a few days. RNA-seq…
Read MoreFree Resources for Teaching Yourself to Analyze Next Gen Sequencing Data
…out the Case Studies on EdX. There is one on RNA-seq data analysis and another on ChIP–seq data analysis. Note: Even if a class is not in progress, you can…
Read MoreAn overview of the Yeast one-hybrid assay
If you are regularly doing ChIP-qPCR, ChIP-RNAseq or luciferase reporter assays to measure protein-DNA interactions, then this article is for you! ChIP experiments can tell you what DNA sequences your…
Read MoreA Microscopy Glossary Part 2: ‘Confocality Means….’
…image chip, which is a square matrix of light-sensitive elements (capacitors), or pixels that convert photons into photoelectrons, which can be subsequently recorded and quantified. The photon count per pixel…
Read MorePathway Analysis for Next Gen Data
Squinting at a long list of significant genes from your latest RNA-seq experiment? Having trouble making sense of the results? You’re not alone. Pathway analysis is becoming increasingly popular because…
Read MoreThree Insights for Choosing the Best DNA Size Selection Method for Your Project
…for a range of applications, and their conclusions provide some useful insight for the community. Double-Digest RAD-Seq Based on the original protocol for restriction site associated DNA (RAD) sequencing, double-digest…
Read MoreSorting Single Cells – What Do You Need to Consider?
…advances in flow sorting technologies, particularly chip-based sorters, offer improved user interfaces at lower costs and with smaller laboratory footprints. We can confidently look forward to continued progress in this…
Read MoreDNA Footprinting
…footprinting assay may seem ancient and complex and is surpassed by newer alternatives and modifications like ChIP–seq, X-ray crystallography, yeast hybrid systems and in silico prediction and modelling softwares, it…
Read MoreIntroduction to DNA Microarrays
…designated locations on the solid surface, usually glass or silicon chip (see Figure 1). Figure 1: A DNA microarray is a collection of synthetic DNA sequences (probes) attached to a…
Read MoreA Protein Renaturation Toolkit: 21 Tips and Tricks for Refolding Proteins
…it in a reaction buffer that differs from the refolding buffer. Tip 7: Use a Microfluidic Chip Another tool worth trying is microfluidic chips. As denatured protein flows on the…
Read MoreHow to Be Greener – The Environmentally Friendly Guide to PCR
…for temperature sensing, the sun for energy and a PCR machine with a magnifying lens and PCR chip. The light is focused by the lens and is then converted into…
Read MoreGo Fishing for Your Favorite Protein with Immunoprecipitation!
…and forms the basis for most colorimetric biosensor chip applications. 2. Chromatin Immunoprecipitation (ChIP) In this method your goal is to demonstrate DNA/protein interactions. To perform ChIP you 1) cross-link…
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