What is deep RNA sequencing?

Deep sequencing refers to sequencing a genomic region multiple times, sometimes hundreds or even thousands of times. This next-generation sequencing (NGS) approach allows researchers to detect rare clonal types, cells, or microbes comprising as little as 1% of the original sample.

Is RNA-Seq deep sequencing?

RNA-Seq is a recently developed approach to transcriptome profiling that uses deep-sequencing technologies. Studies using this method have already altered our view of the extent and complexity of eukaryotic transcriptomes.

How does rip seq work?

RIP-Seq maps the sites at which proteins are bound to the RNA within RNA-protein complexes. In this method, RNA-protein complexes are immunoprecipitated with antibodies targeted to the protein of interest. After RNase digestion, RNA protected by protein binding is extracted and reverse-transcribed to cDNA.

What is ChIP-seq and RNA-Seq?

ChIP-seq is run to map the global binding sites of the studied transcription factor, and RNA-seq is measured from the wild type and knockout model to identify genes regulated by the TF.

How do you analyze RNA-Seq data?

For most RNA‐seq studies, the data analyses consist of the following key steps [5, 6]: (1) quality check and preprocessing of raw sequence reads, (2) mapping reads to a reference genome or transcriptome, (3) counting reads mapped to individual genes or transcripts, (4) identification of differential expression (DE) …

How do you analyze RNA sequencing data?

What is RNA pull down assay?

RNA pull-down assays selectively extract a protein–RNA complex from a sample. Typically, the RNA pull-down assay takes advantage of high affinity tags, such as biotin or azido-phosphine chemistry.

What is the purpose of ChIP-seq?

ChIP-Seq identifies the binding sites of DNA-associated proteins and can be used to map global binding sites for a given protein. ChIP-Seq typically starts with crosslinking of DNA-protein complexes. Samples are then fragmented and treated with an exonuclease to trim unbound oligonucleotides.

What can you do with RNA-Seq data?

Beyond quantifying gene expression, the data generated by RNA-Seq facilitate the discovery of novel transcripts, identification of alternatively spliced genes, and detection of allele-specific expression.