ATAC-Seq - Assay for Transposase-Accessible Chromatin with
high-throughput sequencing. The ATAC-Seq method relies on
next-generation sequencing (NGS) library construction using the
hyperactive transposase Tn5. By sequencing regions of open
chromatin, ATAC-Seq can help to assess genome-wide chromatin
accessibility, thus uncover how chromatin packaging and other factors
affect gene expression.
aseQTLs - allele-specific expression quantitative trait loci, may
result from cis-regulatory SNPs.
ChIP-seq - ChIP-sequencing, is a method used to analyze protein
interactions with DNA. The method combines chromatin
immunoprecipitation (ChIP) with massively parallel DNA sequencing to
identify the binding sites of DNA-associated proteins.
CAGE - Cap analysis of gene expression, is an approach to
identify and monitor the activity (transcription initiation frequency)
of transcription start sites (TSSs) at single base-pair resolution
across the genome.
RAD-seq - a protocol for genotyping and discovery of
single-nucleotide polymorphisms (SNPs) (Baird et al., 2008). This
approach is particularly useful for genotyping when a reference genome
is not available, such as in ecological studies. Restriction site
associated DNA (RAD) markers are a type of genetic marker which are
useful for association mapping, QTL-mapping, population genetics,
ecological genetics and evolutionary genetics. The use of RAD markers
for genetic mapping is often called RAD mapping. An important aspect of
RAD markers and mapping is the process of isolating RAD tags, which are
the DNA sequences that immediately flank each instance of a particular
restriction site of a restriction enzyme throughout the genome. Once
RAD tags have been isolated, they can be used to identify and genotype
DNA sequence polymorphisms mainly in form of single nucleotide
polymorphisms (SNPs). Polymorphisms that are identified and
genotyped by isolating and analyzing RAD tags are referred to as RAD
eeQTL - Exon expression QTL - study the genomic variations
that are associated with splicing regulation. A stringent criterion was
adopted to study gene-level eQTLs and exon-level eeQTLs for both cis-
and trans- factors. (Guan et al, 2014).
eQTL / geQTL - (gene) expression Quantitative Trait Locus, denotes
the relationship between transcription and SNP. An eQTL is a locus that
explains a fraction of the genetic variance of a gene expression
phenotype. It essentially perform a GWAS using the expression value of
the gene as a trait. It usually contains locations where there is
polymorphic expression (Most people do some form of cis-eQTL analysis
using only SNPs within some kMB of the TSS or TSE. Often k=0.5MB).
mQTL / meQTL denotes the relationship between methylation and SNP.
mQTL == Metabolomic Quantitative Trait Loci
miRNA-seq - MicroRNA sequencing, a type of RNA-Seq, is the use of
next-generation sequencing or massively parallel high-throughput DNA
sequencing to sequence microRNAs, also called miRNAs. miRNA-seq differs
from other forms of RNA-seq in that input material is often enriched
for small RNAs. miRNA-seq allows researchers to examine tissue-specific
expression patterns, disease associations, and isoforms of miRNAs, and
to discover previously uncharacterized miRNAs.
RNA-Seq (named as an abbreviation of RNA sequencing) is a
sequencing technique which uses next-generation sequencing (NGS) to
reveal the presence and quantity of RNA in a biological sample at a
given moment, analyzing the continuously changing cellular
transcriptome. Specifically, RNA-Seq facilitates the ability to look at
alternative gene spliced transcripts, post-transcriptional
modifications, gene fusion, mutations/SNPs and changes in gene
expression over time, or differences in gene expression in different
groups or treatments
RACE - Rapid amplification of cDNA ends, is a technique used in
molecular biology to obtain the full length sequence of an RNA
transcript found within a cell.
sQTL - Caused by SNPs that alter splicing or alternative splicing
(AS), such as by changing the sequence-specific binding affinity of
splicing factors to the pre-mRNA.
GWAS denotes the relationship between SNP and trait.
RPKM - Reads Per Kilobase Million:
Total reads in a sample divided by 1,000,000 ➜ "per million" scaling factor (SF);
Divide read counts by SF(normalize for seq depth) ➜ RPM (reads per million);
Divide RPM by the length of the gene (kb) ➜ RPKM.
FPKM - Fragments Per Kilobase Million):
Similar to RPKM but by paired-end RNA-seq fragments, where two reads can correspond
to a single fragment.
TPM - Transcripts Per Kilobase Million):
Divide the read counts by the length of each gene (kb) ➜ reads per kilobase (RPK)
Devide all RPK values in a sample by 1,000,000 ➜ "per million" scaling factor (SF);
Divide the RPK values by SF ➜ TPM.
Version 1: June 17, 2022
Last update: December 16 2022 16:31:29.
Collected and edited by
Dept of Animal Science
Iowa State University
Guan, L., Yang, Q., Gu, M. et al. (2014) Exon expression QTL (eeQTL)
analysis highlights distant genomic variations associated with splicing
regulation. Quant Biol 2, 71–79 (2014).