Genomics Glossary for RNA Sequencing Up Close

base pairs (bp)	Paired nucleotides that make up DNA and RNA. Following specific hydrogen-bonding patterns, DNA has adenine(A)-thymine(T) and guanine(G)-cytosine(C) base pairings. Similarly, RNA has adenine-uracil(U) and guanine-cytosine base pairings
bioinformaticians	scientists with multidisciplinary training in computer science and biology who are equipped to answer important biological questions based on analyzing and interpreting huge biological-based datasets
database	an organized collection of information that can be accessed, managed, and updated
DNA Sequencing	“Reading” the DNA molecule to determine the sequence of the letters
exome	a collection of all the protein-coding sequences (exons) found in the genome. This is the part of the human genome we understand best, but the exome only makes up about 2% of the entire genome.
exons	the pieces of RNA that we keep in the final messenger RNA molecule to code for proteins
flow cell	a special glass plate that is a little larger than a microscope slide, which is used to attach DNA or cDNA (made from RNA) samples to sequence them in next-generation sequencing machines
gene	a unit of DNA that controls specific traits
gene expression	the process by which instructions in our DNA are converted into functional products, such as proteins (read more about the basics of gene expression [1])
gene quantification	counting the number of reads we have assigned to each gene
genome	all the DNA in an organism
genomics	the study of a large number of genes and their interactions and/or of entire genomes (all of the DNA in an organism) to learn what kind of information is coded in these DNA sequences and how the DNA instructions are carried out
hip dysplasia	a hip joint structural problem
hypothesis	an educated guess that can be tested
introns	the pieces of RNA that are removed from final messenger RNAs (these segments are not used to code for proteins)
multimappers	Sequencing reads that align to multiple locations
mutation	alterations in the DNA
nucleotides	the basic structural units of nucleic acids such as DNA and RNA. They are made up of a nucleoside coupled to a phosphate group
paired-end reads	two reads that were sequenced from opposing ends of the same molecule. See paired-end sequencing [2].
paired-end sequencing	a type of sequencing that obtains reads starting from opposing ends of the same molecule. The reads are output as paired-end reads.
primer	short nucleotide sequences that serve as a starting point for DNA synthesis. They are required for DNA replication because DNA polymerase can only add nucleotides to an existing DNA strand.
read alignment, read mapping	The entire process of taking sequencing reads and assigning them to specific locations in the genome
ribonucleic acid (RNA)	a nucleic acid molecule that is implicated in various biological roles, including coding, decoding, regulation, and expression of genes.
RNA sequencing (RNA-seq)	a technique that reveals the presence and quantity of RNA in a biological sample at a given moment in time.
RNA splicing	The process of editing messenger RNA during transcription through removal of introns. Exons are joined together through a process called ligation.
sequencing	The process of determining the order of nucleotides that makes up DNA or RNA
sequencing reads	a list of short nucleotide sequences (100-200 letters, or base pairs (bp)
single-end reads	reads that were sequenced from only one end of the molecule (as opposed to paired-end reads)
spliceforms	different variations of messenger RNA that are produced by the same gene; which specific spliceforms and how much of each type are produced from a gene can change what is translated into proteins; having "alternative spliceforms" is a way a single gene can respond to different biological situations by producing different products using the same string of DNA sequence.
spliceosome	a biological machine made up of RNA and protein complexes which function to remove introns from a trascribed pre-mRNA and then ligate the exons together
string	a sequence of one or more letters
transcription	the process in which information in a strand of DNA is decoded into a messenger RNA molecule