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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
RNA sequencing of isolated and/or microdissected cell nuclei
snRNA-seq, also known as single nucleus RNA sequencing, single nuclei RNA sequencing or sNuc-seq, is an RNA sequencing method for profiling gene expression
SnRNA-seq
Single cell RNA sequencing method
Perturb-seq (also known as CRISP-seq and CROP-seq) refers to a high-throughput method of performing single cell RNA sequencing (scRNA-seq) on pooled genetic
Perturb-seq
Study of RNA transcripts
field: microarrays, which quantify a set of predetermined sequences, and RNA-Seq, which uses high-throughput sequencing to record all transcripts. As the
Transcriptomics_technologies
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
Software project for the analysis of genomic data
analysis of RNA-seq data. It uses a negative binomial distribution modeling for differential expression analysis of read count from RNA-seq data. It is
Bioconductor
Analysis technique of genes
development of high-throughput RNA sequencing (RNA-seq) and microarrays has made gene expression analysis a routine. RNA analysis was previously limited
Single-cell_transcriptomics
Examines sequence information from individual cells
sequences. Several scRNA-seq protocols have been published: Tang et al., STRT, SMART-seq, SORT-seq, CEL-seq, RAGE-seq, Quartz-seq. , and C1-CAGE. These
Single-cell_sequencing
Quantitative, genome-wide transcriptomic technique
3' mRNA-seq is a quantitative, genome-wide transcriptomic technique based on the barcoding of the 3' untranslated region (UTR) of mRNA molecules. Unlike
3'_mRNA-seq
vary. Second, both strands are always sequenced in genome sequencing, but RNA-seq can be strand-specific. Third, transcriptome assembly is more challenging
De novo transcriptome assembly
De_novo_transcriptome_assembly
previous work Bloom filters are also employed in some RNA-Seq pipelines. RNA-Skim clusters RNA transcripts and then uses Bloom filters to find sig-mers:
Bloom filters in bioinformatics
Bloom_filters_in_bioinformatics
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
Software package
It is primarily employed for the analysis of high-throughput RNA sequencing (RNA-seq) data to identify differentially expressed genes between different
DESeq2
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
RNA-Seq. RNA reads may be obtained using a variety of RNA-seq methods. There are a number of public databases that contain freely available RNA-Seq data
Phylogenetic inference using transcriptomic data
Phylogenetic_inference_using_transcriptomic_data
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
MicroRNA_sequencing
Molecular biology technique
active DNA regulatory elements. Integrative analysis combining ATAC-seq with RNA-seq has been used to identify novel oncogenes and elucidate regulatory
ATAC-seq
Technology for RNA sequencing
Bulk RNA barcoding and sequencing (BRB-seq) is an ultra-high-throughput bulk 3' mRNA-seq technology that uses early-stage sample barcoding and unique
BRB-seq
DNA reverse transcribed from RNA
heterologous expression), or to sequence or quantify mRNA molecules using DNA based methods (qPCR, RNA-seq). cDNA that codes for a specific protein can be transferred
Complementary_DNA
popular RNA-seq differential expression (DE) methods blindly without checking the underlying assumptions. For example, in population-scale human RNA-seq samples
Jingyi_Jessica_Li
Cellular biology lab technique
CITE-Seq (Cellular Indexing of Transcriptomes and Epitopes by Sequencing) is a method for performing RNA sequencing along with gaining quantitative and
CITE-Seq
Aspect of genetics
transcriptional analysis of paired-end RNA-seq reads. SplitSeek allows de novo prediction of splice junctions in short-read RNA-seq data, suitable for detection
Chimeric_RNA
Range of methods designed for assigning cell types
developed in the late 1990's (Laser Capture Microdissection) and combined with RNA-seq profiling in 2013 in Michael Eisen's lab using fruit fly embryos. Spatial
Spatial_transcriptomics
Computational technique
process. Single-cell protocols have much higher levels of noise than bulk RNA-seq, so a common step in a single-cell transcriptomics workflow is the clustering
Trajectory_inference
Professor in the Department of Genome Sciences at the University of Washington
open-source software tools for transcriptomics, particularly for RNA-Seq and single-cell RNA-Seq data analysis. His work has been central to the fields of gene
Cole_Trapnell
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)
Small RNA sequencing (Small RNA-Seq) is a type of RNA sequencing based on the use of NGS technologies that allows to isolate and get information about
Small_RNA_sequencing
"FINDER: an automated software package to annotate eukaryotic genes from RNA-Seq data and associated protein sequences". BMC Bioinformatics. 44 (9): e89
List of gene prediction software
List_of_gene_prediction_software
Type of non-coding RNA molecule
genome-wide techniques such as RNA-seq and ChIP-seq. eRNAs can be subdivided into two main classes: 1D eRNAs and 2D eRNAs, which differ primarily in terms
Enhancer_RNA
Techniques used to study microbe gene expression
assembly along with RNA-Seq reads generated from the sample and calculates normalized transcript abundance (meaning the number of RNA-Seq reads cor-responding
Metatranscriptomics
Method used to analyze protein interactions with DNA
ChiRP-Seq to measure RNA-bound DNA and proteins. DRIP-seq uses S9.6 antibody to precipitate three-stranded DND:RNA hybrids called R-loops. TCP-seq, principally
ChIP_sequencing
Type of RNA found in cells
acid (or circRNA) is a type of single-stranded RNA which, unlike linear RNA, forms a covalently closed continuous loop. In circular RNA, the 3' and 5'
Circular_RNA
RNA editing application
are then read through RNA-seq. This technology allows us to glean cell-type specific temporal information associated with RNA-seq data, that until now
RNA_timestamp
Gene prediction algorithm
generated by mapping to the genome short RNA-Seq reads. Extrinsic evidence is not limited to the 'native' RNA sequences. The cross-species proteins collected
GeneMark
Quantity divided by its original amount
is often used in analysis of gene expression data from microarray and RNA-Seq experiments for measuring change in the expression level of a gene. A disadvantage
Fold_change
Topics referred to by the same term
mythology 204 Kallisto, an asteroid HS Kallisto, a Greek warship kallisto, an RNA-Seq bioinformatics tool Kalisto (disambiguation) Callisto (disambiguation)
Kallisto
Gene expression database
Lausanne for retrieval and comparison of gene expression patterns from RNA-Seq, scRNA-Seq, Microarray, In situ hybridization and EST studies, across multiple
Bgee
Conversion of a gene's sequence into a mature gene product or products
also some non-coding RNAs (e.g., snRNAs, snoRNAs or long non-coding RNAs). RNA polymerase III transcribes 5S rRNA, transfer RNA (tRNA) genes, and some small
Gene_expression
American genetics researcher
including RNA-Seq for mapping transcriptomes, NextGen Paired end sequencing for mapping genomes, protein microarrays, and ChIP-Chip (later ChIP-Seq) for globally
Michael_P._Snyder
hybridization assays, such as DNA microarray experiments, RT-qPCR, and RNA-Seq. A spike-in is designed to bind to a DNA molecule with a matching sequence
RNA_spike-in
Loose connective tissue composed mostly by adipocytes
the study of WAT browning. RNA sequencing (RNA-Seq) is a powerful computational tool that allows for the quantification of RNA expression for all genes
Adipose_tissue
Sub-discipline of biology
generation sequencing (NGS) to quantify RNA in samples on a high throughput scale. As biology trends toward using RNA-seq over microarray analysis in evaluating
Degradomics
Gene expression data repository
high-throughput screening genomics data are derived from microarray or RNA-Seq experimental data. These data need to conform to the minimum information
Gene_Expression_Omnibus
Research tool in genomics
massively parallel single-cell RNA-sequencing (RNA-seq). Studies utilising "CRISP-seq", "CROP-seq", and "PERTURB-seq" have demonstrated rich genomic
Genome-wide CRISPR-Cas9 knockout screens
Genome-wide_CRISPR-Cas9_knockout_screens
Different products from the same gene
the surface of the protein. Isoforms at the RNA level are readily characterized by cDNA transcript and RNA-Seq studies. Many human genes possess confirmed
Isoform
technologies (e.g. RNA-Seq) using Bowtie first and then mapping to a reference genome to discover RNA splice sites de novo. TopHat aligns RNA-Seq reads to mammalian-sized
TopHat_(bioinformatics)
sequencing by the Illumina HiSeq platform. A similar method to G&T-seq, developed months earlier, is DR-seq (DNA and RNA sequencing). The primary difference
G&T-seq
Molecule for mRNA-capture
are termed RNA transcript isoforms. The transcriptome is a set of all RNA, including rRNA, mRNA, tRNA, and non-coding RNA. Specifically mRNA transcripts
Transcriptome in vivo analysis tag
Transcriptome_in_vivo_analysis_tag
Process in molecular biology
RNA splicing is a process in molecular biology where a newly-made precursor messenger RNA (pre-mRNA) transcript is transformed into a mature messenger
RNA_splicing
Human gene and protein
on the negative strand in the opposite direction of TMEM269. A study of RNA-seq data according to tissue type in humans found the expression of TMEM269
TMEM269
Small non-coding RNA
glycoRNAs might act as direct ligands for Siglec receptors. GlycoRNAs have the potential to revolutionize the field of RNA sequencing (RNA-Seq) and improve
GlycoRNA
to dNTPs. ClickSeq and Poly(A)-ClickSeq provide specific applications over other common RNA-seq techniques. These include: Removal of RNA fragmentation
ClickSeq
Database of DNA sequencing data
(NCBI) in 2007 in order to provide a repository for data produced by RNA-Seq and ChIP-Seq studies as well as large-scale studies including the Human Microbiome
Sequence_Read_Archive
Concept in molecular biology
single cell RNA seq data. In particular, it enables estimations of RNA velocities of single cells by distinguishing unspliced and spliced mRNAs in standard
RNA_velocity
expression in single-cell RNA-seq (scRNA-seq) and haplotyping via linked reads[clarification needed]. Batch effect Multiplex (assay) BRB-seq König, Julian; Zarnack
Unique_molecular_identifier
English healthcare company
platform can be used for single cell RNA-Seq (scRNA-Seq), single nuclei RNA-Seq (sNuc-Seq), plant protoplast RNA-Seq (ppRNA-Seq) and the encapsulation of cells
Dolomite_Bio
Collection of microscopic DNA spots attached to a solid surface
Advances in massively parallel sequencing has led to the development of RNA-Seq technology, that enables a whole transcriptome shotgun approach to characterize
DNA_microarray
Set of all RNA molecules in one cell or a population of cells
transcriptomics techniques include DNA microarrays and RNA-Seq. Both techniques require RNA isolation through RNA extraction techniques, followed by its separation
Transcriptome
Graph measuring gene relationships
profiling technologies such as Microarray or RNA-Seq. Co-expression networks are used to analyze single cell RNA-Seq data, in order to better characterize the
Gene_co-expression_network
Species of bacterium
sequenced by both industry and academic groups. Furthermore, small RNA data was obtained by RNA-Seq in C. glutamicum ATCC 13032. The metabolism of this strain
Corynebacterium_glutamicum
tissues. RNA-seq data confirm that ZNF816 is broadly expressed at varying levels across tissues. In normal tissues, it shows moderate to high mRNA levels
ZNF816
Application of statistical techniques to biological systems
diseases in human genetics Studies for differential expression of genes from RNA-Seq data, as for RT-qPCR and microarrays, demands comparison of conditions
Biostatistics
Ancient Arabian civilization
"KAPA Stranded mRNA-Seq Kit（KK8420）: de novo RNA-seq (stranded mRNA-Seq) from total RNA derived from invertebrates（stranded mRNA-Seq）". Bio-Protocol.
Dilmun
Species of bacterium
Alcalase by Novozymes. A small antisense RNA against Subtilisin Carlsberg named BLi_r0872 was discovered in an RNA-seq based study. It may have a putative
Bacillus_licheniformis
Cell-free DNA profiling method
assessment of the genes' prognostic importance. EPIC-seq uses machine learning to deduce the RNA expression of the genes and proposes two new metrics:
EPIC-Seq
Single-cell sequencing technology
chromatin velocity with RNA velocity has been proposed to reveal even more information about differentiation pathways. scGET-seq has some of the same limitations
ScGET-seq
French artificial intelligence company
1519–1525 (2019) Schmauch, Benoît et al. “A deep learning model to predict RNA-Seq expression of tumours from whole slide images”, Nature Communications volume
Owkin
Subfield
bulk RNA-seq or dissociated into single cells suspensions in single cell RNA-seq. Although some literature refers to "spatial genomics" for RNA, growing
Spatial_biology
Biological molecules used for experiment calibration
on the application: RNA spike-ins: Commonly used in gene expression studies like RNA-Seq and Microarray analysis. Synthetic RNA molecules of defined
Spike-in_controls
Sequence of DNA that determines traits in an organism
Wold B (July 2008). "Mapping and quantifying mammalian transcriptomes by RNA-Seq". Nature Methods. 5 (7): 621–8. doi:10.1038/nmeth.1226. PMC 13303166. PMID 18516045
Gene
Process by which a gene can code for multiple proteins
diseases is cancer. Abnormally spliced mRNAs are also found in a high proportion of cancerous cells. Combined RNA-Seq and proteomics analyses have revealed
Alternative_splicing
Laboratory technique
results from scRNA-seq to classically defined neuronal cell types is very challenging for all these reasons and additionally single-cell RNA-seq has its own
Patch-sequencing
Description of the structure and function of a genome
because RNAs and proteins are direct products of coding sequences. If RNA-Seq data is available, it may be used to annotate and quantify all of the genes
DNA_annotation
In genetics and biochemistry, determining the structure of an unbranched biopolymer
next-generation sequencing applied to whole transcriptomes see: RNA-Seq and MicroRNA Sequencing. Methods for performing protein sequencing include: Edman
Sequencing
Large-scale deep-learning system developed by DeepMind
concurrently: RNA-seq, CAGE and PRO-cap (gene expression), splice sites, splice site usage and splice junctions (splicing patterns), DNase, ATAC-seq, histone
AlphaGenome
DRIP-seq (DRIP-sequencing) is a technology for genome-wide profiling of a type of DNA-RNA hybrid called an "R-loop". DRIP-seq utilizes a sequence-independent
DRIP-seq
Structure in lactic-acid bacterium RNA
Bouloc P, Lartigue MF, Glaser P (May 2015). "Single nucleotide resolution RNA-seq uncovers new regulatory mechanisms in the opportunistic pathogen Streptococcus
Asd_RNA_motif
positioning from Valouev et al., transcriptional profiling or strand sensitive RNA-Seq with Cloonan et al., single cell transcriptional profiling with Tang et
ABI_Solid_Sequencing
Numerous sRNAs have been identified using both computational analysis and laboratory-based techniques such as Northern blotting, microarrays and RNA-Seq in a
Bacterial_small_RNA
Identification and study of genomic sequences
Alexander; Davis, Carrie A.; et al. (October 2012). "STAR: ultrafast universal RNA-seq aligner". Bioinformatics. 29 (1): 15–21. doi:10.1093/bioinformatics/bts635
Sequence_analysis
American biologist and computer scientist
alignment of NGS sequences to large genomes and for assembly of sequences from RNA-Seq experiments. These became known as the "Tuxedo" suite, including the Bowtie
Steven_Salzberg
Class of ribonucleic acid that is not translated into proteins
RNAs (rRNAs), as well as small RNAs such as microRNAs, siRNAs, piRNAs, snoRNAs, snRNAs, exRNAs, scaRNAs and the long ncRNAs such as Xist, HOTAIR, and MALAT1
Non-coding_RNA
Biomedical engineer
clinical specimens. A widely adopted example is Seq-Well, a low-cost, portable device for single-cell RNA-sequencing designed to work in resource-limited
Alex_K._Shalek
Process of separating populations of cells
single-cell RNA-Seq data to divide the cells into different categories. All the methods are modified to resolve the problems in RNA-Seq data such as
Cell_sorting
2014). "starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data". Nucleic Acids Research. 42
CeRNA_database
Sequence alignment and analysis software
Salzberg, S. L. (16 March 2009). "TopHat: discovering splice junctions with RNA-Seq". Bioinformatics. 25 (9): 1105–1111. doi:10.1093/bioinformatics/btp120
Bowtie_(sequence_analysis)
Field of molecular biology
regulatory regions. These assays include ATAC-seq, DNase-Seq and FAIRE-Seq. Microarrays measure the amount of mRNA in a sample that corresponds to a given gene
Functional_genomics
Computer scientist
While at Harvard, he showed that gene expression data in microarray and RNA-Seq experiments, could be considered approximately low-rank, which could then
Arnav_Kapur
RNA sequences
and structural RNA allows for increased sensitivity in sRNA analysis. Strand-specific RNA-Seq provides further characterization of sRNA by predicting transcript
Anti_small_RNA
Topics referred to by the same term
on engineering Transcripts per million, a measure of gene expression in RNA-Seq Trusted Platform Module, a specification for a secure cryptoprocessor included
TPM
Type of organism
PMID 37761912. Wang, Zhong; Gerstein, Mark; Snyder, Michael (January 2009). "RNA-Seq: a revolutionary tool for transcriptomics". Nature Reviews Genetics. 10
Chemolithoautotroph
Data scientist
between RNA-seq and microarrays", "subSeq: Determining appropriate sequencing depth through efficient read subsampling", "Design and Analysis of Bar-seq Experiments"
David G. Robinson (data scientist)
David_G._Robinson_(data_scientist)
Species of bacteria, cause of plague
Meng X, Ji X, Qu Y, Liu Z, et al. (2013). "Determination of sRNA expressions by RNA-seq in Yersinia pestis grown in vitro and during infection". PLOS
Yersinia_pestis
Evolution of novel genes from non-genic DNA sequence
sequences at the mRNA level may be confirmed individually through techniques such as quantitative PCR, or globally through RNA sequencing (RNA-seq). Similarly
De_novo_gene_birth
Genome research project
cooperation with RefSeq and Uniprot reference annotation databases toward achieving annotation convergence, and the annotation of lncRNAs has been improved
GENCODE
Hashimshony T, Wagner F, Sher N, Yanai I (September 2012). "CEL-Seq: single-cell RNA-Seq by multiplexed linear amplification". Cell Reports. 2 (3): 666–73
List of single cell omics methods
List_of_single_cell_omics_methods
Non-protein coding transcripts longer than 200 nucleotides
ncRNAs from small non-coding RNAs, such as microRNAs (miRNAs), small interfering RNAs (siRNAs), Piwi-interacting RNAs (piRNAs), small nucleolar RNAs (snoRNAs)
Long_non-coding_RNA
Database containing reference sequences of genes, proteins and transcripts
Reference Sequence (RefSeq) database is an open access, annotated and curated collection of publicly available nucleotide sequences (DNA, RNA) and their protein
RefSeq
Single-cell RNA sequencing and dual host-pathogen RNA sequencing are some of the commercially available RNA sequencing technologies. RNA-Seq allows clinicians
Precision_diagnostics
Biological term
or protein coding genes. Small RNA Expression – smRNA-Seq identifies expression of small noncoding RNA, primarily miRNAs. Reference epigenomes for healthy
Epigenome
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