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RIP-chip (RNA immunoprecipitation chip) is a molecular biology technique which combines RNA immunoprecipitation with a microarray. The purpose of this technique is to identify which RNA sequences interact with a particular RNA binding protein of interest in vivo .
Alternative microarray methods have recently been developed, mainly PolII RIP-chip: RNA immunoprecipitation of RNA polymerase II with phosphorylated C-terminal domain directed antibodies and hybridization on a microarray slide or chip (the word chip in the name stems from "ChIP-chip" where a special Affymetrix GeneChip was required). A ...
Microarray and sequencing flow cell. Microarrays and RNA-seq rely on image analysis in different ways. In a microarray chip, each spot on a chip is a defined oligonucleotide probe, and fluorescence intensity directly detects the abundance of a specific sequence (Affymetrix).
RNA-Seq can also be used to determine exon/intron boundaries and verify or amend previously annotated 5' and 3' gene boundaries. Recent advances in RNA-Seq include single cell sequencing, bulk RNA sequencing, [6] 3' mRNA-sequencing, in situ sequencing of fixed tissue, and native RNA molecule sequencing with single-molecule real-time sequencing. [7]
A microarray is a multiplex lab-on-a-chip. [1] Its purpose is to simultaneously detect the expression of thousands of biological interactions. It is a two-dimensional array on a solid substrate—usually a glass slide or silicon thin-film cell—that assays (tests) large amounts of biological material using high-throughput screening miniaturized, multiplexed and parallel processing and ...
DNA:RNA immunoprecipitation followed by hybridization on tiling microarray (DRIP-chip): [3] This method also relies on the use of the S9.6 mAb. However, instead of entering into a sequencing pipeline, the immunoprecipitated material in DRIP-chip is hybridized to a microarray. An advantage of DRIP-chip over DRIP-seq is the rapid obtention of the ...
Whole transcriptome shotgun sequencing (WTSS) [18] is the latest in gene expression studies, using next generation sequencing (NGS) to quantify RNA in samples on a high throughput scale. [19] As biology trends toward using RNA-seq over microarray analysis in evaluating the transcriptome, so does degradomics.
Two principles have been used to develop m5C sequencing methods. The first one is antibody-based approach (bisuphite sequencing and m5C-RIP), similar to m6C sequencing. The second is detecting targets of m5C RNA methyltransferases by covalently linking the enzyme to its target, and then using IP specific to the target enzyme to enrich for RNA ...