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An Introduction To ChIP-seq

…more commonly ChIP is interrogated with microarrays (ChIP-chip) or next-generation sequencing (ChIPseq). How does ChIP-chip work? ChIP-on-chip, or ChIP-chip, combines chromatin immunoprecipitation with microarray (chip) analysis. In 2001, Jason Lieb…

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An 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….

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Generating 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…

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The 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…

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Use 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….

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Analyzing 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…

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All 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…

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Studying 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…

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Top 10 Tips for NGS Library Preparation

…and ChIPseq. 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…

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A 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….

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An 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…

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Pathway 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…

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DNA Footprinting

…footprinting assay may seem ancient and complex and is surpassed by newer alternatives and modifications like ChIPseq, X-ray crystallography, yeast hybrid systems and in silico prediction and modelling softwares, it…

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Introduction 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…

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