Expressed Sequence Tags (ESTs) versus Serial Analysis of Gene Expression

is done to confirm plasmid identities by their amount and size and to examine unknown plas-

Aziz, N., Qin, Z., Bry, L., Driscoll, D. K., Funke, B., Gibson, J. S., & ... Voelkerding, K. V. (2015). College of American Pathologists' Laboratory Standards for Next-Generation Sequencing Clinical Tests. Archives Of Pathology & Laboratory Medicine, 139(4), 481-493 13p.

Molecular Cell Biology, 7th Edition, 2013, Lodish, Berk, Kaiser, Krieger, Bretscher. Ploegh, Amon, and Scott. W.H. Freeman and Company (ISBN-13: 978-1-4292-3413-9)

Finally it was found that a total of 62.1 % to about a 74.7% of the human genome was covered by either proceed or by the help of primary transcript.

This method, as well as the Maxam and Gilbert method, for sequencing DNA are transforming the world of science, medicine and the views of people around the world.

The initial step of Sanger sequencing, designing primer pairs for PCR, is often performed manually, with the aid of software such as Primer-Blast that can analyse only one genetic locus at a time, or PCR Suite, that can analyse more than one locus, but does not check for specificity. The manual design of primer pairs is especially cumbersome and prone to errors for long lists of genetic loci.

Raw data were processed and normalized by the Robust Multichip Averaging (RMA) method (Irizarry et al., 2003) using affy packages of R(v. 3.1.3) (Team, 2004) .The linear regression model package limma (Smyth, 2004) was used to classify chips into each group. The Bayes method (Benjamini and Hochberg, 1995) was used to correct for multiple testing. |logFC| > 2 and P-value < 0.05 were used as cutoff to identify genes which are differentially expressed in

Trimmomatic v.0.36 –REF was used to trim reads by removing leading bases with Phred33 quality scores < 5, trailing bases with Phred33 quality scores < 3, using a sliding window of 4 bases and removing the 5’ terminal base if the average Phred33 score of the 4 bases was < 15, and completely discard trimmed reads with less than 36 remaining bases. The high quality reads were subsequently mapped to the pig genome Sscrofa build 11.1 using the Star software v.2.5.2a and default parameters while simultaneously adding unique read groups to the files – REF. Gene prediction coordinates (release 11.1.90) were obtained from Ensembl (http://www.ensembl.org) Samtools v.1.3.1 –REF was used to merge bams from the same sample and to convert bam files to sam files before HTSeq -REF was run with the reverse stranded option to calculate the number of reads mapped to each gene.

High-throughput genome sequencing technologies are currently the important topic in the biology and medicine that allow us to look at thousands of sequence reads at a time. High-throughput and next generation sequencing technologies have largely been using for standard sequencing applications. Anyway these new technologies bring with many new challenges for biologist and bioinformatics people as how to process and interpret the massive amounts of biological data so as to achieve at biologically significant results. We presented a concise description of most commonly used sequencing technologies and the associated challenges below.

They summarized how various genome-wide tools allow studying the diverse aspects of the epigenome from five different aspects. I am going to focus on three parts of

c. The results were analyzed by 3 steps. First of all, specific regions of the genes were PCR amplified and visualized on the gel. Secondy, T7EN1 cleavage assay were used to detect sgRNA:Cas9 mediated on target cleavage of specific genes. Finally, PCR amplified regions were cloned and sequenced to determine the deletions or insertions.

One of the fundamental discoveries of the 20th century was that DNA was the genetic code’s physical structure (Watson & Crick, 1953) and, since then, many studies have disclosed the complicated pattern of regulation and expression of genes, which involve RNA synthesis and its subsequent translation into proteins.

Due to our profound genomic studies, we have been able to sequence many genomes of various organisms. With the

The Encyclopedia of DNA Elements (ENCODE) is a project designed to compare and contrast the repertoire of RNAs produced by the human cells and cross verify with other methods like NGS. After a five year start-up since the beginning of the ENCODE project just 1% of the human genome has been observed and what was achieved was just the confirmation of the results of previous studies.

It is a simple technique to understand and use, and it produces results rapidly (Vogel et al., 2012). It is highly sensitive, with the potential to produce millions to billions of copies of a specific product for sequencing, cloning, and analysis. This is true of qPCR as well, but qPCR has the advantage of quantification of the synthesized product. Thus, it can be used to analyze alterations of gene expression levels in tumors, microbes, or other disease states.