lncRNAs	long non-coding RNAs
LPS	lipopolysaccharide
RNA-seq	RNA-sequencing
bp	base pair
NGS	next-generation sequencing
CPAT	Coding-Potential Assessment Tool
CPC	Coding Potential Calculator
FEELnc	Flexible Extraction of LncRNAs
Pfam	protein family database
DELs	differentially expressed lncRNAs
GO	Gene Ontology database
TAR	transcriptionally active region
DEGs	differentially expressed genes
SNV	single nucleotide variant
SNP	single nucleotide polymorphism
PGE2	prostaglandin E2
TNF-α	tumor necrosis factor alpha
IL-1β	interleukin 1 beta
IL-6	interleukin 6
IFNs	interferons
PCA	principal component analysis
FPKM	fragments per kilobase of transcript per million mapped reads
FDR	false discovery rate
AS	alternative splicing
rMATS	replicate multivariate analysis of transcript splicing
DAS	differentially alternative splicing
A5SS	alternative 5′splice site
A3SS	alternative 3′splice site
MXE	mutually exclusive exons
RI	retention intron
SE	skipping exon
AF	alternative first
AL	last exon
PSI	percent splicing inclusion
SSR	single sequence repeat
ASE	allele-specific expression
AAF	alternative allele fraction
TLR	Toll-like receptor
I 5	intron 5
dsRNA	double stranded RNA
SINE	short interspersed nuclear element
A-to-I	adenosine to inosine RNA editing
T4	thyroxine
T3	triiodothyronine
MXC-I	major histocompatibility complex I
RhoGTPases	Rho family of GTPase
MAPK	mitogen-activated protein kinas
NF-κB	nuclear factor kappa-light-chain-enhancer of activated B cells
JNK	c-Jun N-terminal kinases
RIG-I signaling pathway	Retinoic acid-Inducible Gene I signaling pathway
heteroref	heterozygous variants in which reference allele was predominant
heteroalt	heterozygous variants in which alternate allele was predominant
true heterozygotes	heterozygous sites with no predominant variant
GATK	The Genome Analysis Toolkit
ΔPSI	difference in PSI values
BP	biological process
MF	molecular function
CC	cellular components
ΔΔCT	comparative cycle threshold method
rs ID	SNP annotation in database
C-to-U	cytidine to uridine RNA editing
VEP	Variant Effect Predictor
VCF	variant calling format
r	Pearson’s correlation coefficient
KEGG	Kyoto Encyclopaedia of Genes and Genomes database
GO	Gene Ontology
ENA	European Nucleotide Archive