This unit describes ChIP-Seq methodology, which involves chromatin immunoprecipitation (ChIP) followed by high-throughput sequencing (Seq), and enables the genome-wide identification of binding sites of transcription factors (TFs) and other DNA-binding proteins. The process is initiated by cross-linking DNA and DNA-bound proteins. Subsequently, chromatin is isolated from nuclei and subjected to...

Identifying binding locations of transcription factors (TFs) within long segments of noncoding DNA is a challenging task. Recent chromatin immunoprecipitation on microarray (ChIP-chip) experiments utilizing tiling arrays are especially promising for this task since they provide high-resolution genome-wide maps of the interactions between the TFs and the DNA. Data from these experiments are inva...

A tetrakis-acridinyl peptide (TAP) cassette, consisting of a double-stranded region of alternating AT sequence bound to TAP and a single stranded overhanging sequence of continuous dA, was prepared by mixing TAP with d[A18(TA)51]. A TAP cassette could be applied to the fluorometric detection of hybridized DNA on the DNA chip, which was prepared by stamping a 45-meric DNA probe onto a gold-coate...

Detecting high-risk (HR) HPV is important for clinical management of women with persistent HPV-positive and Pap-negative results. The Cobas 4800 HPV test is the first FDA-approved HPV DNA test that can be used alone as a first-line screening tool. The HPV 9G DNA chip test is a PCR-based DNA microarray assay. We evaluated the patients of consecutive HPV-positivity on HPV 9G DNA chip test without...

The main aim of this paper is to study the material removal phenomenon using the finite element method (FEM) analysis for orthogonal cutting, and the impact of cutting speed variation on the chip formation, stress and plastic deformation. We have explored different constitutive models describing the tool-workpiece interaction. The Johnson-Cook constitutive model with damage initiation and damag...

Recent developments on various lab-on-a-chip techniques allow miniaturized and integrated devices to perform on-chip single-molecule studies. Fluidic-based platforms that utilize unique microscale fluidic behavior are capable of conducting single-molecule experiments with high sensitivities and throughputs, while biomolecular systems can be studied on-chip using techniques such as DNA curtains,...

Abstract This chip provides retinal and simple cell responses to visual stimuli. It can be used by visual physiologists to debug and test their experimental setups and by instructors to demonstrate the responses of the early visual system. The chip has a hexagonal arrangement of 7 photodiodes. Subsequent processing produces the chip’s outputs: An adaptive photoreceptor cell, a retinal horizonta...

UNLABELLED hmChIP is a database of genome-wide chromatin immunoprecipitation (ChIP) data in human and mouse. Currently, the database contains 2016 samples from 492 ChIP-seq and ChIP-chip experiments, representing a total of 170 proteins and 11 069 914 protein-DNA interactions. A web server provides interface for database query. Protein-DNA binding intensities can be retrieved from individual sa...