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Time-resolved RNA sequencing methods are applications of RNA-seq that allow for observations of RNA abundances over time in a biological sample or samples
Time-resolved_RNA_sequencing
Lab technique in cellular biology
RNA-Seq (short for RNA sequencing) is a next-generation sequencing (NGS) technique used to quantify and identify RNA molecules in a biological sample,
RNA-Seq
Range of methods designed for assigning cell types
hybridization RNA-Seq Single cell sequencing Single-cell transcriptomics Visible Embryo Project Spatial biology "Method of the Year 2020: spatially resolved transcriptomics"
Spatial_transcriptomics
Examines sequence information from individual cells
million mRNA bases. Usually, a mix of millions of cells is used in sequencing the DNA or RNA using traditional methods like Sanger sequencing or next generation
Single-cell_sequencing
DNA sequencing
elusive. Third generation sequencing technologies hold promising prospects in resolving this issue by enabling sequencing of mRNA molecules at their full
Third-generation_sequencing
DNA / RNA sequencing technique
Nanopore sequencing is a third generation approach used in the sequencing of biopolymers — specifically, polynucleotides in the form of DNA or RNA. Nanopore
Nanopore_sequencing
RNA-Seq is a technique that allows transcriptome studies (see also Transcriptomics technologies) based on next-generation sequencing technologies. This
List of RNA-Seq bioinformatics tools
List_of_RNA-Seq_bioinformatics_tools
Single cell RNA sequencing method
CROP-seq) refers to a high-throughput method of performing single cell RNA sequencing (scRNA-seq) on pooled genetic perturbation screens. Perturb-seq combines
Perturb-seq
Single-Cell RNA-Sequencing Method
Drop-Seq is a high-throughput, single-cell RNA sequencing (scRNA-seq) technology used to analyze the mRNA expression of thousands of individual cells by
Drop-Seq
RNA component of the ribosome, essential for protein synthesis in all living organisms
transfer RNA (tRNA) and messenger RNA (mRNA) to process and translate the latter into proteins. Ribosomal RNA is the predominant form of RNA found in
Ribosomal_RNA
Study of genes found in the environment
Metagenomic sequencing is particularly useful in the study of viral communities. As viruses lack a shared universal phylogenetic marker (as 16S RNA for bacteria
Metagenomics
Molecular biology technique
; Henttinen, S.; Kaarijärvi, R. (2021-09-06). "Single-cell ATAC and RNA sequencing reveal pre-existing and persistent cells associated with prostate cancer
ATAC-seq
Identification and study of genomic sequences
used at this stage depend on the sequencing platform. For instance, FastQC checks the quality of short reads (including RNA sequences), Nanoplot or PycoQC
Sequence_analysis
Sequencing of amino acid arrangement in a protein
Protein sequencing is the practical process of determining the amino acid sequence of all or part of a protein or peptide. This may serve to identify the
Protein_sequencing
DNA sequencing method
Circular consensus sequencing (CCS) is a DNA sequencing method that is used in conjunction with single-molecule real-time sequencing to yield highly accurate
Circular_consensus_sequencing
Experimental process
has been done on ribosomes, viral RNA, and single-stranded RNA structures within viruses. These studies have resolved structural features at different
Nucleic acid structure determination
Nucleic_acid_structure_determination
Methodology for biomedical research
readout of thousands of sgRNA CRISPR perturbations by in situ sequencing of sgRNA and barcode sequences amplified from mRNA using a molecular inversion
Optical_pooled_screening
DNA sequencing method
can also be used for whole-genome and region sequencing, transcriptome analysis, metagenomics, small RNA discovery, methylation profiling, and genome-wide
Illumina_dye_sequencing
Biological term
hypersensitive sites Sequencing (DNase-Seq) uses the DNase I enzyme to find open or accessible regions in the genome. Gene Expression – RNA-Seq and expression
Epigenome
Method for separation and analysis of biomolecules
electrophoresis method for separation and analysis of biomacromolecules (DNA, RNA, proteins, etc.) and their fragments, based on their size and charge through
Gel_electrophoresis
Small non-coding ribonucleic acid molecule
the mRNA. miRNAs resemble the small interfering RNAs (siRNAs) of the RNA interference (RNAi) pathway, except miRNAs derive from regions of RNA transcripts
MicroRNA
Genomic technique
microarrays (ChIP-on-chip), molecular cloning and sequencing, or direct high-throughput sequencing (ChIP-Seq).[citation needed] Native ChIP is mainly
Chromatin_immunoprecipitation
In DNA sequencing, a read is an inferred sequence of base pairs (or base pair probabilities) corresponding to all or part of a single DNA fragment. A typical
Read_(biology)
This list of RNA structure prediction software is a compilation of software tools and web portals used for nucleic acid structure prediction. The single
List of RNA structure prediction software
List_of_RNA_structure_prediction_software
response can surprisingly be much different. Sequencing technologies such as 16S rRNA shotgun metagenomic sequencing have facilitated the rapid expansion of
Pharmacomicrobiomics
International scientific research project (1990–2003)
meet the high-throughput demands of genome sequencing projects. Beginning in 2008, a new technology known as RNA-seq was introduced that allowed scientists
Human_Genome_Project
Genetic testing technique
AN, Moffitt JR, Wang S, Zhuang X (April 2015). "RNA imaging. Spatially resolved, highly multiplexed RNA profiling in single cells". Science. 348 (6233)
Fluorescence in situ hybridization
Fluorescence_in_situ_hybridization
Structure in molecular biology
central channel between each pair of tetrads. They can be formed of DNA, RNA, LNA, and PNA, and may be intramolecular, bimolecular, or tetramolecular
G-quadruplex
Genetic technique for identifying organisms in mixed samples
Metabarcoding is the barcoding of DNA/RNA (or eDNA/eRNA) in a manner that allows for the simultaneous identification of many taxa within the same sample
Metabarcoding
Protein-coding gene in humans
"G3BP-driven RNP granules promote inhibitory RNA-RNA interactions resolved by DDX3X to regulate mRNA translatability". Molecular Cell. 85 (3): 585–601
DDX3X
archaeal DNA is copied into a newly synthesized strand of RNA using the sole Pol II-like RNA polymerase (RNAP). The process occurs in three main steps:
Archaeal_transcription
detect the presence of larger mRNA molecules or assembled into two-dimensional microarrays for high-throughput sequencing analysis. oligosaccharide A polymeric
Glossary of cellular and molecular biology (M–Z)
Glossary_of_cellular_and_molecular_biology_(M–Z)
Techniques used to study microbe gene expression
obtained by capturing the total mRNA of the microbiome and performing whole-metatranscriptomics shotgun sequencing. Although microarrays can be exploited
Metatranscriptomics
exonuclease-treated ends are determined using some combination of DNA sequencing, microarrays, and PCR. These sequences are then mapped to the genome to
ChIP-exo
Method of genome sequencing
Genome skimming is a sequencing approach that uses low-pass, shallow sequencing of a genome (up to 5%), to generate fragments of DNA, known as genome skims
Genome_skimming
American biotechnology company
small ribonucleic acid (sRNA) analysis. In June 2009, Illumina announced the launch of their own Personal Full Genome Sequencing Service at a depth of 30X
Illumina,_Inc.
Portion of gene's sequence which codes for protein
prediction uses sampling and sequencing of mRNA from cells, although there is still the problem of determining which parts of a given mRNA are actually translated
Coding_region
Process of copying a segment of DNA into RNA
RNA for the purpose of gene expression. Some segments of DNA are transcribed into RNA molecules that can encode proteins, called messenger RNA (mRNA)
Transcription_(biology)
Community of microorganisms
this applies to 16S rRNA amplicon sequencing as well and is a fundamental problem. With shotgun sequencing, it can be resolved by having a high coverage
Microbiota
Technique used for species identification and phylogenetic studies
even to species level. It is conducted using DNA or RNA followed by amplification and sequencing of specific, conserved regions in the diatom genome followed
Algae_DNA_barcoding
Austrian biologist and friar (1822–1884)
unconscious adjustment of his observations". Several writers have attempted to resolve this paradox. One attempted explanation invokes confirmation bias. Fisher
Gregor_Mendel
Study of biochemical processes in an individual cell
genomics are applied to the cDNA to make sequencing possible. Alternatively, fluorescent compounds attached to RNA hybridization probes are used to identify
Single-cell_analysis
Family of DNA sequences found in prokaryotic organisms
E. coli cut the CRISPR RNA precursor within the repeats into mature spacer-containing RNA molecules called CRISPR RNA (crRNA), which remained bound to
CRISPR
Set of standards
molecular-weight size marker, also referred to as a protein ladder, DNA ladder, or RNA ladder, is a set of standards that are used to identify the approximate size
Molecular-weight_size_marker
Software in bioinformatics
Dunn et al. "Phased diploid genome assembly with single-molecule real-time sequencing." Nature methods 13, no. 12 (2016): 1050-1054. Available here Kolmogorov
De_novo_sequence_assemblers
Complete set of nucleic acid sequences for humans
processing. Noncoding genes include those for tRNAs, ribosomal RNAs, microRNAs, snRNAs and long non-coding RNAs (lncRNAs). The number of reported non-coding genes
Human_genome
Cellular process of protein synthesis
produced using RNA molecules as templates. The generated protein is a sequence of amino acids determined by the sequence of nucleotides in the RNA. The nucleotides
Translation_(biology)
Method of species identification using a short section of DNA
barcoding techniques were developed from early DNA sequencing work on microbial communities using the 5S rRNA gene. In 2003, specific methods and terminology
DNA_barcoding
Protein found in humans
conserved folded RNA recognition motifs spanning residues 106–176 (RRM1) and 191–259 (RRM2), respectively, required to bind target RNA and DNA; an unstructured
TAR_DNA-binding_protein_43
Bioinformatics company
Generation Sequencing Analysis product 2010 Integromics publication in Nature describes new class of gene-termini-associated human RNAs suggests a novel RNA copying
Integromics
Protein-coding gene in the species Homo sapiens
Bradfield J, Guo Y, Toskala E, Otieno FG, et al. (2013). "Whole-genome DNA/RNA sequencing identifies truncating mutations in RBCK1 in a novel Mendelian disease
RBCK1
Technique in molecular biology
Chromatin Interaction Analysis by Paired-End Tag Sequencing (ChIA-PET or ChIA-PETS) is a technique in molecular biology that incorporates chromatin immunoprecipitation
ChIA-PET
Chinese scientist
vivo RNA structurome. In particular her work on a high throughput method, Structure-seq, to resolve one of the first two genome-wide in vivo RNA structure
Yiliang_Ding
Biotechnological procedure
quantify and clonally amplify nucleic acids strands including DNA, cDNA, or RNA. The key difference between dPCR and qPCR lies in the method of measuring
Digital polymerase chain reaction
Digital_polymerase_chain_reaction
DNA sequences with no known biological function
Additionally, non-protein coding regions such as genes for ribosomal RNA and transfer RNA, regulatory sequences, origins of replication, centromeres, telomeres
Junk_DNA
Process of identifying pollen donor plant species
identifying pollen donor plant species through the amplification and sequencing of specific, conserved regions of plant DNA. Being able to accurately
Pollen_DNA_barcoding
Field of study
Single-molecule real-time sequencing (SMRT) is a single-molecule DNA sequencing method. Single-molecule real-time sequencing utilizes a zero-mode waveguide
Epigenomics
Collection of techniques used to analyze biological markers in the genome and proteome
cancer will likely to focus on the Next Generation Sequencing (NGS). By utilizing DNA and RNA sequencing to do cancer diagnostics, technology in the field
Molecular_diagnostics
International research consortium
promoter properties, exon length and pseudo-messenger RNA. The rise of next-generation sequencing was significantly beneficial to the advancement of CAGE
FANTOM
History of the field of study
After the 1970s, nucleic acid sequencing allowed molecular evolution to reach beyond proteins to highly conserved ribosomal RNA sequences, the foundation
History of molecular evolution
History_of_molecular_evolution
Human infectious disease
viral RNA involved. This had resulted in disagreement with respect to molecular classification of this virus, a situation which has been resolved with
Hepatitis_D
Utilizing polymers to examine small biological samples
fluorescence microscopy of RNA molecules, which in turn led to spatially precise in situ sequencing, namely ExSeq (expansion sequencing), in 2021. Even with
Expansion_microscopy
Classification by similarity of DNA
(sometimes over 100) marker genes can be used at the same time, producing highly resolved phylogenies that correctly identify problematic taxa. It is
Operational_taxonomic_unit
Digital nucleic acid sequence database
fragments depends on the sequencing platform and bioinformatic methods available at the time. For assemblies that are not fully resolved, summary statistics
Reference_genome
Genus of viruses
orthoflavivirus, orthoflaviviral or orthoflaviviruses) is a genus of positive-strand RNA viruses in the family Flaviviridae. The genus includes the West Nile virus
Orthoflavivirus
Technology for examining cells
microscopy, and sequencing-based methods like assigning unique barcodes to DNA or tissue dissection followed by traditional methylation sequencing approaches
Spatial DNA methylation profiling
Spatial_DNA_methylation_profiling
light-switchable molecules designed for in-cell applications and time-resolved techniques to study RNA folding. Light sheet fluorescence microscopy for the observation
Cluster of Excellence Frankfurt Macromolecular Complexes
Cluster_of_Excellence_Frankfurt_Macromolecular_Complexes
Region within a prokaryotic cell containing genetic material
functional arrangement with the help of chromosomal architectural proteins and RNA molecules as well as DNA supercoiling. Genome length varies widely (generally
Nucleoid
Observation of the diversity of tumour cells
developed that attempt to resolve clonal structure using allele frequencies for the observed mutations. Single-cell sequencing is a new technique that is
Tumour_heterogeneity
Genetic trait
of gene regulation; for example, mapping RNA-sequencing data can help determine the effects of variants on mRNA expression levels, which then presumably
Complex_traits
Queueing of ribosomes during protein synthesis
reveal pausing sites through sequencing the ribosome protected fragments (RPFs or footprints) to map ribosome occupancy on the mRNA. Ribosome profiling has
Ribosomal_pause
Species of virus
earlier genesis. The virus is an enveloped, positive-sense, single-stranded RNA virus which enters its host cell by binding to the N-acetyl-9-O-acetylneuraminic
Human_coronavirus_HKU1
Hybrid mammal
produced from a natural breeding. The study also discovered through sequencing 16S ribosomal RNA encoding genes that the F1 hybrids all have an intestinal microbiome
Coywolf
Technique used to measure similarity in DNA sequences
"Non-radioactive hybridization probes prepared by the chemical labelling of DNA and RNA with a novel reagent, photobiotin". Nucleic Acids Research. 13 (3): 745–761
DNA–DNA_hybridization
(Variable Number Tandem Repeat) regions mapping, RNA sequencing mapping, chromatin immunoprecipitation and sequencing analysis were also reported. [citation needed]In
Human_Pangenome_Reference
Region of often-methylated DNA with a cytosine followed by a guanine
indicated 11 microRNAs whose promoters were hypermethylated in colon cancers at frequencies between 50% and 100% of cancers. MicroRNAs (miRNAs) are small endogenous
CpG_site
Medical condition
novel etiological class of intellectual disability syndromes tied to an RNA/DNA-binding protein. Clinically, the syndrome is characterized by developmental
PURA_syndrome
Type of non-invasive imaging technique
fluorochromes can bind to antibodies, RNA, and DNA to fluoresce and quantify data DNA Sequencing: Sanger Sequencing is a common form of nucleic acid detection
Fluorescence_imaging
is found in cell nucleus and that RNA is present exclusively in the cytoplasm. At the time, "yeast nucleic acid" (RNA) was thought to occur only in plants
Timeline of the history of genetics
Timeline_of_the_history_of_genetics
Family of short non-coding RNA fragments
to establish which is prominent in a sample simply by sequencing the small RNA content. The miRNAs of oncomir-1 and its paralogs are likely contribute to
Mir-92 microRNA precursor family
Mir-92_microRNA_precursor_family
Monitoring wastewater for contaminants
populations, detection of new pathogen mutations and variants by genomic sequencing, and to detect the presence of psychoactive drugs. CDC states that wastewater
Wastewater_surveillance
Repeated DNA variation between individuals
genome using SNPs as markers. Next-generation sequencing techniques including short and long read sequencing are nowadays increasingly used and have begun
Copy_number_variation
Famous mycologist
before the advent of gene sequencing. Once gene sequencing became possible he would later determine that DNA recombination was time consuming and only useful
Cletus_P._Kurtzman
Oldest cultured human cell line (1951)
been present. Another genome sequencing project from 2013 dealt with the different HeLa Kyoto lineage. It did not resolve the haplotype but instead analyzed
HeLa
for ribosomal RNA (rRNA) targets, commonly used for detecting bacteria. rRNA are very abundant in the cell comprising about 80% of the RNA content of the
MAGIChip
either at the same time or consecutively. antisense See template strand. antisense RNA (asRNA) A single-stranded non-coding RNA molecule containing an
Glossary of cellular and molecular biology (0–L)
Glossary_of_cellular_and_molecular_biology_(0–L)
Evolution of the primate transcriptome Matthias Mann Organellar and time resolved proteomics Anna Tramontano Progress, assessment and perspectives in
List of Intelligent Systems for Molecular Biology keynote speakers
List_of_Intelligent_Systems_for_Molecular_Biology_keynote_speakers
2004 book on evolution by Richard Dawkins & Yan Wong
enterobacteria phage Qbeta, and found it was subject to variation and selection. RNA can catalyze chemical reactions (like an enzyme) and store information (like
The_Ancestor's_Tale
Extinct species of mammal from Australasia
development. In 2023, RNA was extracted from a 130-year-old thylacine specimen in Sweden; this represented the first time RNA has been extracted from
Thylacine
Genus of flagellate intestinal eukaryotes parasitic in various vertebrates
Giardia assemblages (species/clades) have been identified based on genome sequencing; each assemblage has been assigned a letter between A and H. Every assemblage
Giardia
Long-term oceanographic study by the Bermuda Institute of Ocean Sciences
fluorescence. Based on epifluorescence microscopy and viral phoH gene sequencing, the abundance and composition of viruses in the Sargasso Sea has been
Bermuda Atlantic Time-series Study
Bermuda_Atlantic_Time-series_Study
Epidemiological instrument for finding substances
2013 study of archived wastewater samples from the Netherlands found viral RNA of Aichivirus A in Dutch sewage samples dating back to 1987, two years prior
Wastewater-based_epidemiology
Technique to separate DNA or RNA fragments
electrophoresis of nucleic acids is an analytical technique to separate DNA or RNA fragments by size and reactivity. Nucleic acid molecules are placed on a
Gel electrophoresis of nucleic acids
Gel_electrophoresis_of_nucleic_acids
American biologist (1928–2025)
molecular biology History of RNA biology Life Story – 1987 BBC docudrama about Watson and Crick's discovery of DNA structure List of RNA biologists Nobel disease –
James_Watson
Very large DNA virus
aminoacyl tRNA synthetases, enzymes that catalyze the esterification of specific amino acids or their precursors to their corresponding cognate tRNAs to form
Giant_virus
Repeating sequences of 2–13 base pairs of DNA
method of RNA splicing is believed to have diverged from human evolution at the formation of tetrapods and to represent an artifact of an RNA world. Almost
Microsatellite
Branch of phylogeny that analyzes genetic, hereditary molecular differences
recent times largely by DNA sequencing, which produces the exact sequences of nucleotides or bases in either DNA or RNA segments extracted using different
Molecular_phylogenetics
Species of bacterium
in EBPR was elucidated using culture-independent approaches such as 16S rRNA clone banks that showed the Betaproteobacteria dominated lab-scale EBPR reactors
Accumulibacter_phosphatis
Type of vaccine for humans
synthetic mRNA platforms that they had developed, modified mRNA (modRNA), uridine RNA (uRNA), self-amplifying mRNA (saRNA) and trans-amplifying mRNA (taRNA). Using
Pfizer–BioNTech COVID-19 vaccine
Pfizer–BioNTech_COVID-19_vaccine
Domain of organisms
cell walls, 2. two unusual coenzymes, 3. results of 16S ribosomal RNA gene sequencing. To emphasize this difference, Woese, Otto Kandler and Mark Wheelis
Archaea
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