What is dUTP method?
In the dUTP method, second-strand cDNA is synthesized in the presence of dUTP and fragmented by sonication, followed by the standard Illumina library preparation procedure and subsequent degradation of dU-containing second strands by USER. Read_1 indicates the reads in the direction of transcription.
What is strand specific RNA sequencing?
Strand-specific RNA-Seq allows for sense and antisense transcript structures to be predicted, overlapping regions of transcription can be identified exactly and expression levels of sense and antisense genes can be more accurately estimated.
What are transcriptome sequences?
Transcriptome sequencing employs high-throughput sequencing technologies to get access to almost all transcripts of specific tissues or cells in a certain state by comprehensive and rapid cDNA sequencing, becoming the basis as well as the starting point for the research of gene expression.
How does Whole transcriptome sequencing work?
Whole transcriptome sequencing By looking at the whole transcriptome, researchers are able to determine global expression levels of each transcript, identify exons, introns and map their boundaries. In addition, RNA-Seq can be used for the identification of splicing variants.
Can cDNA be sequenced?
The sequencing of cDNAs can be carried out to obtain two levels of information (Fig. 3). The full‐length sequencing of cDNAs is performed to determine the complete sequence of the protein coding as well as the non‐coding parts of the mRNA in question.
What is the difference between cDNA and genomic DNA?
The main difference between cDNA and genomic DNA is that cDNA represents the transcriptome of a particular organism whereas genomic DNA represents the genome.
What is stranded vs Unstranded RNA-seq?
The read ambiguity in stranded RNA-seq arises only from overlapping genes transcribed from the same strand. In contrast, for non-stranded RNA-seq, the ambiguity arises from both the overlapping genes on the same strand and also from the opposite strands.
What is strand specific DNA sequencing?
Strand specific libraries allow you to identify the coding DNA strand for the transcript you sequence, while the strand information is lost in what you call regular library protocols. Neither polyA selection nor ribo-minus gives you information or limits to whether or not you will create a stranded library.
What can a transcriptome tell us?
What can a transcriptome tell us? An RNA sequence mirrors the sequence of the DNA from which it was transcribed. Consequently, by analyzing the entire collection of RNA sequences in a cell (the transcriptome) researchers can determine when and where each gene is turned on or off in the cells and tissues of an organism.
What is whole transcriptome shotgun sequencing?
In simple words, whole transcriptome shotgun sequencing helps make a blueprint of the transcriptome that includes the entire population of cellular RNAs (mRNA, tRNA, and rRNA). This makes it possible to determine the level of gene expression and the status and timing of gene activation patterns.