Source 1primary paper2018Botanical studies
Toolkit/RNA sequencing
RNA sequencing
Also known as: high-throughput RNA-Seq analyses, RNA-seq, RNA sequencing
Taxonomy: Technique Branch / Method. Workflows sit above the mechanism and technique branches rather than replacing them.
Summary
RNA sequencing (RNA-seq) is a transcriptomic assay method that quantifies gene-expression changes by sequencing RNA-derived libraries. In the cited study, it was used on adult rat amygdala tissue to detect subtle expression changes associated with development, cellular function, and nervous system disease after gestational high-THC cannabis smoke exposure.
Usefulness & Problems
Why this is useful
RNA-seq is useful for measuring transcriptome-wide molecular effects of biological perturbations in tissue samples. In the provided evidence, it enabled detection of subtle amygdala gene-expression changes in adult male offspring following gestational cannabis smoke exposure.
Problem solved
This assay addresses the problem of identifying molecular transcriptional changes in complex tissues after experimental or environmental perturbation. Here, it was applied to reveal amygdala expression changes linked to developmental and nervous system-related categories after prenatal high-THC cannabis smoke exposure.
Problem links
RNA-seq is a scalable discovery assay for making one major class of biomolecular actors, transcripts, visible across many genes at once. It does not solve protein, lipid, or metabolite invisibility directly, but it is a plausible partial tool for multiplex molecular profiling in cells.
RNA-seq could help characterize how closely organoids, ex vivo tissues, or alternative animal models recapitulate human transcriptional states, which is directly relevant to judging model adequacy. It is especially useful for systematic comparison across candidate models and perturbations.
enables broader discovery of specific lncRNAs across physiological and pathological processes
LiteratureIt helps discover candidate lncRNAs involved in physiological and pathological processes, including those relevant to vision.
Source:
It helps discover candidate lncRNAs involved in physiological and pathological processes, including those relevant to vision.
measures genome-wide gene expression changes associated with infection
LiteratureIt provides a broad readout of host gene-expression changes at the infection site in a natural reservoir host.
Source:
It provides a broad readout of host gene-expression changes at the infection site in a natural reservoir host.
measures transcriptome-wide changes after KCl, bicuculline, and TTX-withdrawal stimulation
LiteratureIt solves the need to measure broad transcriptional responses to different neuronal activation paradigms and maturation states.
Source:
It solves the need to measure broad transcriptional responses to different neuronal activation paradigms and maturation states.
provides transcriptome-wide measurement of gene expression changes under different red:blue light ratios
LiteratureIt addresses the question of whether light quality is associated with transcriptomic changes linked to cucumber sex determination and flowering-related pathways.
Source:
It addresses the question of whether light quality is associated with transcriptomic changes linked to cucumber sex determination and flowering-related pathways.
provides transcriptomic readout of molecular effects after gestational cannabis smoke exposure
LiteratureIt provides a molecular readout to complement behavioral phenotyping in offspring exposed during gestation.
Source:
It provides a molecular readout to complement behavioral phenotyping in offspring exposed during gestation.
reveals transcriptomic differences that challenge the view of astrocytes as a homogeneous population
LiteratureIt helps detect transcript-level heterogeneity across astrocytes and supports claims of brain area- and disease-specific properties.
Source:
It helps detect transcript-level heterogeneity across astrocytes and supports claims of brain area- and disease-specific properties.
testing functional transcriptomic consequences of conditional ZFHX3 loss in the SCN
LiteratureIt tests how conditional loss of ZFHX3 changes daily gene expression programs in the SCN.
Source:
It tests how conditional loss of ZFHX3 changes daily gene expression programs in the SCN.
testing functional transcriptomic consequences of ZFHX3 loss
LiteratureIt tests how conditional loss of ZFHX3 affects the SCN transcriptome and circadian gene-expression programs.
Source:
It tests how conditional loss of ZFHX3 affects the SCN transcriptome and circadian gene-expression programs.
Published Workflows
Objective: To characterize the transcriptomic response in ear skin of wild bank voles infected with B. afzelii and identify molecular processes associated with infection in a natural reservoir host.
Why it works: The workflow combines transcriptome-wide measurement with co-expression and enrichment analyses to move from gene-level changes to coordinated biological processes associated with infection status.
B-cell activity and antibody productionsuppressed pro-inflammatory responseextracellular matrix organization changesRNA sequencingweighted gene co-expression network analysisenrichment analysis
Stages
- 1.Transcriptome profiling of infected and uninfected ear skin(broad_screen)
This stage provides the primary data needed to compare infected and uninfected bank vole skin at the site of infection.
Selection: Measure transcriptome-wide expression differences associated with infection status in ear skin.
- 2.Co-expression module discovery(secondary_characterization)
This stage summarizes transcriptomic structure beyond single-gene changes by identifying infection-correlated modules.
Selection: Identify gene modules positively or negatively correlated with infection status.
- 3.Pathway enrichment interpretation(functional_characterization)
This stage converts gene-level and module-level signals into interpretable host-response mechanisms.
Selection: Interpret differentially expressed genes and modules in terms of biological processes and pathways.
Steps
- 1.Perform RNA sequencing on ear skin from infected and uninfected wild bank volesassay used to profile host transcriptomes
Generate transcriptomic data for comparing infection-associated expression states in skin.
This is the foundational measurement step that produces the data required for all downstream analyses.
- 2.Apply weighted gene co-expression network analysis to identify infection-correlated modulescomputational analysis method
Identify coordinated gene modules associated positively or negatively with infection status.
This analysis depends on the transcriptomic profiles generated in the prior sequencing step.
- 3.Perform enrichment analysis to interpret infection-associated genes and modules
Map transcriptomic changes onto biological processes and pathways relevant to host response.
This interpretive step follows gene-level and module-level analyses so the authors can infer biological programs associated with infection.
Objective: To analyze how neuronal maturation and different activity-induction protocols shape electrophysiological and transcriptional responses in primary neuronal cultures.
Why it works: The workflow compares early and mature neuronal cultures and applies distinct stimulation paradigms that trigger different firing patterns, then measures electrophysiological and transcriptomic outputs to resolve whether maturation state and stimulus identity produce distinct transcriptional programs.
activity-dependent transcriptionstimulus-specific firing-pattern-dependent gene regulationtranscription-dependent plasticity mechanismscompound-based neuronal stimulationelectrophysiological comparisonRNA-Seqpost-hoc bioinformatic analysis
Stages
- 1.Developmental-stage comparison under KCl and bicuculline stimulation(functional_characterization)
This stage tests whether neuronal developmental stage changes the response to commonly used activation protocols.
Selection: Compare electrophysiological and transcriptional responses between 7 DIV and 21 DIV neuronal primary cultures after KCl and bicuculline stimulation.
- 2.Stimulus-specific transcriptional profiling in mature neurons(secondary_characterization)
This stage resolves how distinct stimuli that trigger different firing patterns shape transcriptional programs in more developmentally advanced neurons.
Selection: Treat mature neurons with KCl, bicuculline, and TTX-withdrawal and assess transcriptional changes by RNA-Seq.
Steps
- 1.Compare 7 DIV and 21 DIV neuronal cultures under KCl and bicuculline stimulationstimulation conditions
Assess how neuronal maturation influences electrophysiological and transcriptional responses to commonly used activation protocols.
The study first establishes whether developmental stage alters responses before expanding stimulus comparisons in mature neurons.
- 2.Treat mature neurons with KCl, bicuculline, and TTX-withdrawalstimulation conditions
Elicit different firing patterns in mature neurons for stimulus-specific transcriptional comparison.
After establishing that maturation matters, the study focuses on mature neurons to compare multiple stimuli that trigger different firing patterns.
- 3.Assess transcriptional changes by RNA-Seq and post-hoc bioinformatic analysistranscriptomic assay and analysis method
Measure and compare transcriptional profiles, temporal dynamics, and gene-group activation across stimulation conditions.
Transcriptomic analysis follows stimulation so that stimulus-evoked gene expression programs can be quantified and compared.
Objective: Define how ZFHX3 affects the mouse SCN at genomic and transcriptomic levels by combining genome-wide binding-site mapping with time-series transcriptome profiling after conditional loss of ZFHX3.
Why it works: The workflow pairs ChIP-seq to localize ZFHX3 binding in SCN chromatin with RNA-seq across six times-of-day to test functional consequences of ZFHX3 loss on daily transcriptional programs.
ZFHX3 occupancy near transcription start sitespartnership with CLOCK and BMAL1regulation of TTFL genes and clock-controlled geneschromatin immunoprecipitation sequencingtime-series RNA sequencingcontrol versus conditional null comparison
Stages
- 1.Genome-wide mapping of ZFHX3-binding sites in SCN chromatin(functional_characterization)
This stage establishes where ZFHX3 binds genome-wide in the SCN before testing transcriptional consequences.
Selection: Map genomic localization of ZFHX3-binding sites in SCN chromatin.
- 2.Time-series transcriptomic comparison of control and ZFHX3-conditional null SCN(confirmatory_validation)
This stage tests whether the genomic occupancy of ZFHX3 corresponds to functional effects on daily SCN gene expression.
Selection: Test for function by comparing SCN transcriptional profiles of control and ZFHX3-conditional null mutants at six distinct times-of-day.
Objective: Define how ZFHX3 affects the suprachiasmatic nucleus at genomic and transcriptomic levels by mapping ZFHX3 binding sites and testing functional consequences of conditional ZFHX3 loss across the day.
Why it works: The workflow combines genomic localization of ZFHX3 binding with time-resolved transcriptome profiling after conditional loss of ZFHX3, allowing the authors to connect occupancy patterns to functional transcriptional consequences in the SCN.
promoter-proximal ZFHX3 occupancypartnership with CLOCK and BMAL1regulation of TTFL genes and clock-controlled genesChIP-seqRNA-seq
Stages
- 1.Map ZFHX3 genomic localization in SCN chromatin(functional_characterization)
This stage establishes where ZFHX3 binds in SCN chromatin before testing functional consequences.
Selection: genomic localization of ZFHX3 binding sites
- 2.Test functional transcriptomic consequences across time of day(secondary_characterization)
This stage tests whether ZFHX3 loss changes SCN gene expression and daily rhythmic transcription after binding-site mapping.
Selection: differences in SCN transcriptional profiles between control and ZFHX3-conditional null mutants across six times-of-day
Steps
- 1.Perform ChIP-seq on SCN chromatin to map ZFHX3 binding sitesassay used to map genomic localization
Determine genome-wide localization of ZFHX3 binding sites in SCN chromatin.
The abstract presents genomic localization mapping first, before functional testing, to define where ZFHX3 binds.
- 2.Perform RNA-seq at six distinct times-of-day on control and ZFHX3-conditional null SCN samplesassay used for functional transcriptome comparison
Test functional consequences of ZFHX3 loss on SCN transcriptional profiles and circadian expression.
The abstract explicitly states this was done to test for function after mapping genomic localization.
Objective: To test whether different red:blue light ratios are associated with cucumber sex differentiation and to identify transcriptomic changes linked to that response.
Why it works: The study compares shoot-apex transcriptomes between two light-quality conditions to connect phenotypic differences in sex differentiation with differential gene expression and pathway-level changes.
plant hormone signal transductionauxin-associated differential expressiontranscription factor expression changesflowering-time gene upregulationhigh-throughput RNA-Seqcomparative transcriptome analysis
Objective: Discover and study lncRNAs relevant to visual maintenance and impairment.
Why it works: The abstract states that cheaper RNA-seq has enabled widely applied high-throughput screening, which in turn has identified large numbers of specific lncRNAs across physiological and pathological processes.
gene regulationcell proliferationapoptosisdifferentiationimmune responsesoxidative stressinflammationRNA-seqhigh-throughput screening
Stages
- 1.lncRNA discovery by RNA-seq-supported high-throughput screening(broad_screen)
This stage exists to find specific lncRNAs relevant to biological and disease processes before deeper visual-system interpretation or modulation.
Selection: identification of large numbers of specific lncRNAs in physiological or pathological processes
- 2.precise modulation and interpretation in visual maintenance and impairment(functional_characterization)
After candidate lncRNAs are identified, the review's stated focus is to understand their precise modulation in visual maintenance and impairment.
Selection: assessment of lncRNA roles in visual maintenance and impairment
- 3.translation toward diagnostic, prognostic, and therapeutic application(decision_gate)
The review highlights future directions in patients and frames lncRNAs as potentially useful for diagnostic, prognostic, and therapeutic applications.
Selection: potential patient relevance of lncRNAs
Taxonomy & Function
Primary hierarchy
Technique Branch
Method: A concrete measurement method used to characterize an engineered system.
Target processes
recombinationselectiontranscriptionInput: Light
Implementation Constraints
cofactor dependency: cofactor requirement unknownencoding mode: genetically encodedimplementation constraint: context specific validationimplementation constraint: spectral hardware requirementoperating role: sensor
The available evidence supports use of RNA-derived sequencing libraries on adult rat amygdala tissue. No further implementation details, including RNA input requirements, platform, strandedness, or analysis workflow, are provided in the supplied sources.
The supplied evidence does not provide technical details such as library preparation, sequencing depth, read type, normalization strategy, or statistical thresholds. In the cannabis-exposure study, the reported molecular effects were subtle and observed in a subset of male offspring, which may limit generalizability.
Validation
Cell-freeBacteriaMammalianMouseHumanTherapeuticIndep. Replication
Supporting Sources
Source 2review2016Journal of Medical Genetics
Source 3primary paper2023MED
Source 4review2019Annual Review of Neuroscience
Source 5primary paper2026MED
Source 6primary paper2023PPR
Source 7primary paper2025MED
Ranked Claims
Weighted gene co-expression network analysis identified five gene modules correlated positively or negatively with infection status.
Weighted gene co-expression network analysis identified five gene modules, which were positively or negatively correlated with infection status.
infection-correlated gene modules 5
In ear skin of wild bank voles, B. afzelii infection was associated with 54 differentially expressed genes relative to uninfected animals.
We identified 54 differentially expressed genes, of which 37 showed upregulation, and 17 showed downregulation in infected voles compared to uninfected ones.
differentially expressed genes 54downregulated genes 17upregulated genes 37
ChIP-seq mapped genome-wide ZFHX3-binding sites in SCN chromatin, with occupancy predominantly around gene transcription start sites and co-localization with known histone modifications.
ChIP-seq mapped genome-wide ZFHX3-binding sites in SCN chromatin, with occupancy predominantly around gene transcription start sites and co-localization with known histone modifications.
ChIP-seq mapped genome-wide ZFHX3-binding sites in SCN chromatin, with occupancy predominantly around gene transcription start sites and co-localization with known histone modifications.
ChIP-seq mapped genome-wide ZFHX3-binding sites in SCN chromatin, with occupancy predominantly around gene transcription start sites and co-localization with known histone modifications.
ChIP-seq mapped genome-wide ZFHX3-binding sites in SCN chromatin, with occupancy predominantly around gene transcription start sites and co-localization with known histone modifications.
ChIP-seq mapped genome-wide ZFHX3-binding sites in SCN chromatin, with occupancy predominantly around gene transcription start sites and co-localization with known histone modifications.
ChIP-seq mapped genome-wide ZFHX3-binding sites in SCN chromatin, with occupancy predominantly around gene transcription start sites and co-localization with known histone modifications.
Adult conditional loss of ZFHX3 dramatically alters the SCN transcriptome, including neuropeptide neurotransmitter system transcripts and attenuation of daily Bmal1 oscillation.
Adult conditional loss of ZFHX3 dramatically alters the SCN transcriptome, including neuropeptide neurotransmitter system transcripts and attenuation of daily Bmal1 oscillation.
Adult conditional loss of ZFHX3 dramatically alters the SCN transcriptome, including neuropeptide neurotransmitter system transcripts and attenuation of daily Bmal1 oscillation.
Adult conditional loss of ZFHX3 dramatically alters the SCN transcriptome, including neuropeptide neurotransmitter system transcripts and attenuation of daily Bmal1 oscillation.
Adult conditional loss of ZFHX3 dramatically alters the SCN transcriptome, including neuropeptide neurotransmitter system transcripts and attenuation of daily Bmal1 oscillation.
Adult conditional loss of ZFHX3 dramatically alters the SCN transcriptome, including neuropeptide neurotransmitter system transcripts and attenuation of daily Bmal1 oscillation.
Adult conditional loss of ZFHX3 dramatically alters the SCN transcriptome, including neuropeptide neurotransmitter system transcripts and attenuation of daily Bmal1 oscillation.
Cannabis-exposed offspring performed better on visual pairwise discrimination and reversal learning tasks in touchscreen-equipped operant conditioning chambers.
Cannabis-exposed offspring performed better on visual pairwise discrimination and reversal learning tasks in touchscreen-equipped operant conditioning chambers.
Cannabis-exposed offspring performed better on visual pairwise discrimination and reversal learning tasks in touchscreen-equipped operant conditioning chambers.
Cannabis-exposed offspring performed better on visual pairwise discrimination and reversal learning tasks in touchscreen-equipped operant conditioning chambers.
Cannabis-exposed offspring performed better on visual pairwise discrimination and reversal learning tasks in touchscreen-equipped operant conditioning chambers.
Cannabis-exposed offspring performed better on visual pairwise discrimination and reversal learning tasks in touchscreen-equipped operant conditioning chambers.
Cannabis-exposed offspring performed better on visual pairwise discrimination and reversal learning tasks in touchscreen-equipped operant conditioning chambers.
Cannabis-exposed offspring performed better on visual pairwise discrimination and reversal learning tasks in touchscreen-equipped operant conditioning chambers.
RNA sequencing of adult amygdala revealed subtle gene-expression changes related to development, cellular function, and nervous system disease in a subset of male offspring after gestational cannabis smoke exposure.
RNA sequencing of adult amygdala revealed subtle gene-expression changes related to development, cellular function, and nervous system disease in a subset of male offspring after gestational cannabis smoke exposure.
RNA sequencing of adult amygdala revealed subtle gene-expression changes related to development, cellular function, and nervous system disease in a subset of male offspring after gestational cannabis smoke exposure.
RNA sequencing of adult amygdala revealed subtle gene-expression changes related to development, cellular function, and nervous system disease in a subset of male offspring after gestational cannabis smoke exposure.
RNA sequencing of adult amygdala revealed subtle gene-expression changes related to development, cellular function, and nervous system disease in a subset of male offspring after gestational cannabis smoke exposure.
RNA sequencing of adult amygdala revealed subtle gene-expression changes related to development, cellular function, and nervous system disease in a subset of male offspring after gestational cannabis smoke exposure.
RNA sequencing of adult amygdala revealed subtle gene-expression changes related to development, cellular function, and nervous system disease in a subset of male offspring after gestational cannabis smoke exposure.
RNA sequencing of adult amygdala revealed subtle gene-expression changes related to development, cellular function, and nervous system disease in a subset of male offspring after gestational cannabis smoke exposure.
Recent availability of RNA sequencing, immunohistochemistry, electron microscopy, morphological reconstruction, and imaging data has challenged the view that astrocytes are a homogeneous population across the CNS.
Light-quality effects on cucumber sex differentiation might be induced by plant hormone signal transduction and transcription factors.
Thus, sex differentiation affected by light quality might be induced by plant hormone signal transduction and transcription factors.
Light-quality effects on cucumber sex differentiation might be induced by plant hormone signal transduction and transcription factors.
Thus, sex differentiation affected by light quality might be induced by plant hormone signal transduction and transcription factors.
Light-quality effects on cucumber sex differentiation might be induced by plant hormone signal transduction and transcription factors.
Thus, sex differentiation affected by light quality might be induced by plant hormone signal transduction and transcription factors.
Light-quality effects on cucumber sex differentiation might be induced by plant hormone signal transduction and transcription factors.
Thus, sex differentiation affected by light quality might be induced by plant hormone signal transduction and transcription factors.
Light-quality effects on cucumber sex differentiation might be induced by plant hormone signal transduction and transcription factors.
Thus, sex differentiation affected by light quality might be induced by plant hormone signal transduction and transcription factors.
Auxin-related DEGs formed the highest percentage among DEGs in plant hormone signal transduction after treatment.
The specific DEGs related with auxin formed the highest percentage of DEGs in the plant hormone signal transduction.
Auxin-related DEGs formed the highest percentage among DEGs in plant hormone signal transduction after treatment.
The specific DEGs related with auxin formed the highest percentage of DEGs in the plant hormone signal transduction.
Auxin-related DEGs formed the highest percentage among DEGs in plant hormone signal transduction after treatment.
The specific DEGs related with auxin formed the highest percentage of DEGs in the plant hormone signal transduction.
Auxin-related DEGs formed the highest percentage among DEGs in plant hormone signal transduction after treatment.
The specific DEGs related with auxin formed the highest percentage of DEGs in the plant hormone signal transduction.
Auxin-related DEGs formed the highest percentage among DEGs in plant hormone signal transduction after treatment.
The specific DEGs related with auxin formed the highest percentage of DEGs in the plant hormone signal transduction.
Up-regulation and down-regulation of specific DEGs after the light treatments were primarily attributed to plant hormone signal transduction.
the transcriptome analysis showed that up-regulation and down-regulation of specific DEGs (the differentially expressed genes) were primarily the result of plant hormone signal transduction after treatments.
Up-regulation and down-regulation of specific DEGs after the light treatments were primarily attributed to plant hormone signal transduction.
the transcriptome analysis showed that up-regulation and down-regulation of specific DEGs (the differentially expressed genes) were primarily the result of plant hormone signal transduction after treatments.
Up-regulation and down-regulation of specific DEGs after the light treatments were primarily attributed to plant hormone signal transduction.
the transcriptome analysis showed that up-regulation and down-regulation of specific DEGs (the differentially expressed genes) were primarily the result of plant hormone signal transduction after treatments.
Up-regulation and down-regulation of specific DEGs after the light treatments were primarily attributed to plant hormone signal transduction.
the transcriptome analysis showed that up-regulation and down-regulation of specific DEGs (the differentially expressed genes) were primarily the result of plant hormone signal transduction after treatments.
Up-regulation and down-regulation of specific DEGs after the light treatments were primarily attributed to plant hormone signal transduction.
the transcriptome analysis showed that up-regulation and down-regulation of specific DEGs (the differentially expressed genes) were primarily the result of plant hormone signal transduction after treatments.
Cheaper RNA-seq has helped make high-throughput screening of lncRNAs widely applied and has enabled identification of large numbers of specific lncRNAs.
Approval Evidence
8 sources9 linked approval claimsfirst-pass slugs rna-seq, rna-sequencing
Here, we used RNA sequencing to explore the transcriptomic response in the ear skin of wild bank voles infected with B. afzelii.
Source:
the transcriptional changes were assessed by RNA-Seq and post-hoc bioinformatic analysis
Source:
To test for function, we then conducted comprehensive RNA sequencing at six distinct times-of-day to compare the SCN transcriptional profiles of control and ZFHX3-conditional null mutants.
Source:
Analysis of gene expression in the adult amygdala using RNA sequencing revealed subtle changes
Source:
To test for function, we then conducted comprehensive RNA sequencing at six distinct times-of-day to compare the SCN transcriptional profiles of control and ZFHX3-conditional null mutants.
Source:
this view has been challenged in the last few years with the availability of RNA sequencing
Source:
we performed high-throughput RNA-Seq analyses, which compared the transcriptomes of shoot apices between R2B1-treated and R4B1-treated cucumber seedlings
Source:
With the help of cheaper RNA-seq, high-throughput screening of lncRNAs has become widely applied and has identified large numbers of specific lncRNAs in various physiological or pathological processes.
Source:
differential expression resultsupports
In ear skin of wild bank voles, B. afzelii infection was associated with 54 differentially expressed genes relative to uninfected animals.
We identified 54 differentially expressed genes, of which 37 showed upregulation, and 17 showed downregulation in infected voles compared to uninfected ones.
Source:
perturbation effectsupports
Adult conditional loss of ZFHX3 dramatically alters the SCN transcriptome, including neuropeptide neurotransmitter system transcripts and attenuation of daily Bmal1 oscillation.
Source:
stimulus specific transcriptionsupports
In 21 DIV neurons, KCl, bicuculline, and TTX-withdrawal induce specific transcriptional profiles with unique temporal dynamics and activation of different gene groups.
observed that KCl, Bic and TTXw, which trigger different firing patterns, induce specific transcriptional profiles with unique temporal dynamics and activating a variety of gene groups
Source:
molecular effectsupports
RNA sequencing of adult amygdala revealed subtle gene-expression changes related to development, cellular function, and nervous system disease in a subset of male offspring after gestational cannabis smoke exposure.
Source:
field summarysupports
Recent availability of RNA sequencing, immunohistochemistry, electron microscopy, morphological reconstruction, and imaging data has challenged the view that astrocytes are a homogeneous population across the CNS.
Source:
mechanistic hypothesissupports
Light-quality effects on cucumber sex differentiation might be induced by plant hormone signal transduction and transcription factors.
Thus, sex differentiation affected by light quality might be induced by plant hormone signal transduction and transcription factors.
Source:
pathway enrichmentsupports
Auxin-related DEGs formed the highest percentage among DEGs in plant hormone signal transduction after treatment.
The specific DEGs related with auxin formed the highest percentage of DEGs in the plant hormone signal transduction.
Source:
pathway interpretationsupports
Up-regulation and down-regulation of specific DEGs after the light treatments were primarily attributed to plant hormone signal transduction.
the transcriptome analysis showed that up-regulation and down-regulation of specific DEGs (the differentially expressed genes) were primarily the result of plant hormone signal transduction after treatments.
Source:
method enables discoverysupports
Cheaper RNA-seq has helped make high-throughput screening of lncRNAs widely applied and has enabled identification of large numbers of specific lncRNAs.
Source:
Comparisons
Source-stated alternatives
The web research summary mentions single-cell RNA-seq as a higher-resolution comparator in related human skin studies, but this paper itself reports bulk RNA sequencing.; The paper contrasts RNA-seq with ChIP-seq by using the latter for binding-site localization and RNA-seq for functional transcriptome effects.; The abstract contrasts RNA-Seq-based transcriptional assessment with electrophysiological response measurements, but does not name alternative transcriptomic assays.; The abstract pairs RNA-seq with ChIP-seq, where ChIP-seq maps binding and RNA-seq measures transcriptional consequences.; No direct alternative molecular assay is named in the abstract.; The abstract contrasts RNA sequencing with immunohistochemistry, electron microscopy, morphological reconstruction, and imaging as other evidence sources for astrocyte diversity.; No direct alternative assay is named in the abstract.; No explicit alternative discovery methods are named in the abstract.
Source:
The web research summary mentions single-cell RNA-seq as a higher-resolution comparator in related human skin studies, but this paper itself reports bulk RNA sequencing.
Source:
The paper contrasts RNA-seq with ChIP-seq by using the latter for binding-site localization and RNA-seq for functional transcriptome effects.
Source:
The abstract contrasts RNA-Seq-based transcriptional assessment with electrophysiological response measurements, but does not name alternative transcriptomic assays.
Source:
The abstract pairs RNA-seq with ChIP-seq, where ChIP-seq maps binding and RNA-seq measures transcriptional consequences.
Source:
No direct alternative molecular assay is named in the abstract.
Source:
The abstract contrasts RNA sequencing with immunohistochemistry, electron microscopy, morphological reconstruction, and imaging as other evidence sources for astrocyte diversity.
Source:
No direct alternative assay is named in the abstract.
Source:
No explicit alternative discovery methods are named in the abstract.
Source-backed strengths
The cited evidence shows that RNA-seq could detect subtle gene-expression changes in adult amygdala tissue rather than only large transcriptional shifts. The broader claims provided also indicate that RNA sequencing can capture substantial transcriptome alterations, such as dramatic changes in the SCN transcriptome and attenuation of daily Bmal1 oscillation after conditional loss of ZFHX3.
Compared with assays
The abstract contrasts RNA-Seq-based transcriptional assessment with electrophysiological response measurements, but does not name alternative transcriptomic assays.
Shared frame: source-stated alternative in extracted literature
Strengths here: enabled identification of 54 differentially expressed genes in infected versus uninfected voles; captures transcriptome-wide changes across six distinct times-of-day; supports comparison of specific transcriptional profiles and temporal dynamics across stimuli.
Relative tradeoffs: the abstract does not specify single-cell resolution or cell-type-resolved readouts; the abstract does not specify which altered transcripts are direct versus indirect ZFHX3 targets; the abstract does not specify sequencing depth, sampling times, or analysis pipeline details.
Source:
The abstract contrasts RNA-Seq-based transcriptional assessment with electrophysiological response measurements, but does not name alternative transcriptomic assays.
Compared with chromatin immunoprecipitation
The paper contrasts RNA-seq with ChIP-seq by using the latter for binding-site localization and RNA-seq for functional transcriptome effects.; The abstract pairs RNA-seq with ChIP-seq, where ChIP-seq maps binding and RNA-seq measures transcriptional consequences.
Shared frame: source-stated alternative in extracted literature
Strengths here: enabled identification of 54 differentially expressed genes in infected versus uninfected voles; captures transcriptome-wide changes across six distinct times-of-day; supports comparison of specific transcriptional profiles and temporal dynamics across stimuli.
Relative tradeoffs: the abstract does not specify single-cell resolution or cell-type-resolved readouts; the abstract does not specify which altered transcripts are direct versus indirect ZFHX3 targets; the abstract does not specify sequencing depth, sampling times, or analysis pipeline details.
Source:
The paper contrasts RNA-seq with ChIP-seq by using the latter for binding-site localization and RNA-seq for functional transcriptome effects.
Source:
The abstract pairs RNA-seq with ChIP-seq, where ChIP-seq maps binding and RNA-seq measures transcriptional consequences.
Compared with chromatin immunoprecipitation sequencing
The paper contrasts RNA-seq with ChIP-seq by using the latter for binding-site localization and RNA-seq for functional transcriptome effects.; The abstract pairs RNA-seq with ChIP-seq, where ChIP-seq maps binding and RNA-seq measures transcriptional consequences.
Shared frame: source-stated alternative in extracted literature
Strengths here: enabled identification of 54 differentially expressed genes in infected versus uninfected voles; captures transcriptome-wide changes across six distinct times-of-day; supports comparison of specific transcriptional profiles and temporal dynamics across stimuli.
Relative tradeoffs: the abstract does not specify single-cell resolution or cell-type-resolved readouts; the abstract does not specify which altered transcripts are direct versus indirect ZFHX3 targets; the abstract does not specify sequencing depth, sampling times, or analysis pipeline details.
Source:
The paper contrasts RNA-seq with ChIP-seq by using the latter for binding-site localization and RNA-seq for functional transcriptome effects.
Source:
The abstract pairs RNA-seq with ChIP-seq, where ChIP-seq maps binding and RNA-seq measures transcriptional consequences.
Compared with electron microscopy
The abstract contrasts RNA sequencing with immunohistochemistry, electron microscopy, morphological reconstruction, and imaging as other evidence sources for astrocyte diversity.
Shared frame: source-stated alternative in extracted literature
Strengths here: enabled identification of 54 differentially expressed genes in infected versus uninfected voles; captures transcriptome-wide changes across six distinct times-of-day; supports comparison of specific transcriptional profiles and temporal dynamics across stimuli.
Relative tradeoffs: the abstract does not specify single-cell resolution or cell-type-resolved readouts; the abstract does not specify which altered transcripts are direct versus indirect ZFHX3 targets; the abstract does not specify sequencing depth, sampling times, or analysis pipeline details.
Source:
The abstract contrasts RNA sequencing with immunohistochemistry, electron microscopy, morphological reconstruction, and imaging as other evidence sources for astrocyte diversity.
Compared with imaging
The abstract contrasts RNA sequencing with immunohistochemistry, electron microscopy, morphological reconstruction, and imaging as other evidence sources for astrocyte diversity.
Shared frame: source-stated alternative in extracted literature
Strengths here: enabled identification of 54 differentially expressed genes in infected versus uninfected voles; captures transcriptome-wide changes across six distinct times-of-day; supports comparison of specific transcriptional profiles and temporal dynamics across stimuli.
Relative tradeoffs: the abstract does not specify single-cell resolution or cell-type-resolved readouts; the abstract does not specify which altered transcripts are direct versus indirect ZFHX3 targets; the abstract does not specify sequencing depth, sampling times, or analysis pipeline details.
Source:
The abstract contrasts RNA sequencing with immunohistochemistry, electron microscopy, morphological reconstruction, and imaging as other evidence sources for astrocyte diversity.
Compared with imaging surveillance
The abstract contrasts RNA sequencing with immunohistochemistry, electron microscopy, morphological reconstruction, and imaging as other evidence sources for astrocyte diversity.
Shared frame: source-stated alternative in extracted literature
Strengths here: enabled identification of 54 differentially expressed genes in infected versus uninfected voles; captures transcriptome-wide changes across six distinct times-of-day; supports comparison of specific transcriptional profiles and temporal dynamics across stimuli.
Relative tradeoffs: the abstract does not specify single-cell resolution or cell-type-resolved readouts; the abstract does not specify which altered transcripts are direct versus indirect ZFHX3 targets; the abstract does not specify sequencing depth, sampling times, or analysis pipeline details.
Source:
The abstract contrasts RNA sequencing with immunohistochemistry, electron microscopy, morphological reconstruction, and imaging as other evidence sources for astrocyte diversity.
Compared with immunohistochemistry
The abstract contrasts RNA sequencing with immunohistochemistry, electron microscopy, morphological reconstruction, and imaging as other evidence sources for astrocyte diversity.
Shared frame: source-stated alternative in extracted literature
Strengths here: enabled identification of 54 differentially expressed genes in infected versus uninfected voles; captures transcriptome-wide changes across six distinct times-of-day; supports comparison of specific transcriptional profiles and temporal dynamics across stimuli.
Relative tradeoffs: the abstract does not specify single-cell resolution or cell-type-resolved readouts; the abstract does not specify which altered transcripts are direct versus indirect ZFHX3 targets; the abstract does not specify sequencing depth, sampling times, or analysis pipeline details.
Source:
The abstract contrasts RNA sequencing with immunohistochemistry, electron microscopy, morphological reconstruction, and imaging as other evidence sources for astrocyte diversity.
Compared with microscopy
The abstract contrasts RNA sequencing with immunohistochemistry, electron microscopy, morphological reconstruction, and imaging as other evidence sources for astrocyte diversity.
Shared frame: source-stated alternative in extracted literature
Strengths here: enabled identification of 54 differentially expressed genes in infected versus uninfected voles; captures transcriptome-wide changes across six distinct times-of-day; supports comparison of specific transcriptional profiles and temporal dynamics across stimuli.
Relative tradeoffs: the abstract does not specify single-cell resolution or cell-type-resolved readouts; the abstract does not specify which altered transcripts are direct versus indirect ZFHX3 targets; the abstract does not specify sequencing depth, sampling times, or analysis pipeline details.
Source:
The abstract contrasts RNA sequencing with immunohistochemistry, electron microscopy, morphological reconstruction, and imaging as other evidence sources for astrocyte diversity.
Compared with morphological reconstruction
The abstract contrasts RNA sequencing with immunohistochemistry, electron microscopy, morphological reconstruction, and imaging as other evidence sources for astrocyte diversity.
Shared frame: source-stated alternative in extracted literature
Strengths here: enabled identification of 54 differentially expressed genes in infected versus uninfected voles; captures transcriptome-wide changes across six distinct times-of-day; supports comparison of specific transcriptional profiles and temporal dynamics across stimuli.
Relative tradeoffs: the abstract does not specify single-cell resolution or cell-type-resolved readouts; the abstract does not specify which altered transcripts are direct versus indirect ZFHX3 targets; the abstract does not specify sequencing depth, sampling times, or analysis pipeline details.
Source:
The abstract contrasts RNA sequencing with immunohistochemistry, electron microscopy, morphological reconstruction, and imaging as other evidence sources for astrocyte diversity.
Compared with single-cell RNA-seq analysis
The web research summary mentions single-cell RNA-seq as a higher-resolution comparator in related human skin studies, but this paper itself reports bulk RNA sequencing.
Shared frame: source-stated alternative in extracted literature
Strengths here: enabled identification of 54 differentially expressed genes in infected versus uninfected voles; captures transcriptome-wide changes across six distinct times-of-day; supports comparison of specific transcriptional profiles and temporal dynamics across stimuli.
Relative tradeoffs: the abstract does not specify single-cell resolution or cell-type-resolved readouts; the abstract does not specify which altered transcripts are direct versus indirect ZFHX3 targets; the abstract does not specify sequencing depth, sampling times, or analysis pipeline details.
Source:
The web research summary mentions single-cell RNA-seq as a higher-resolution comparator in related human skin studies, but this paper itself reports bulk RNA sequencing.
Compared with single-cell RNA sequencing
The web research summary mentions single-cell RNA-seq as a higher-resolution comparator in related human skin studies, but this paper itself reports bulk RNA sequencing.
Shared frame: source-stated alternative in extracted literature
Strengths here: enabled identification of 54 differentially expressed genes in infected versus uninfected voles; captures transcriptome-wide changes across six distinct times-of-day; supports comparison of specific transcriptional profiles and temporal dynamics across stimuli.
Relative tradeoffs: the abstract does not specify single-cell resolution or cell-type-resolved readouts; the abstract does not specify which altered transcripts are direct versus indirect ZFHX3 targets; the abstract does not specify sequencing depth, sampling times, or analysis pipeline details.
Source:
The web research summary mentions single-cell RNA-seq as a higher-resolution comparator in related human skin studies, but this paper itself reports bulk RNA sequencing.
Compared with single-cell transcriptomics
The web research summary mentions single-cell RNA-seq as a higher-resolution comparator in related human skin studies, but this paper itself reports bulk RNA sequencing.
Shared frame: source-stated alternative in extracted literature
Strengths here: enabled identification of 54 differentially expressed genes in infected versus uninfected voles; captures transcriptome-wide changes across six distinct times-of-day; supports comparison of specific transcriptional profiles and temporal dynamics across stimuli.
Relative tradeoffs: the abstract does not specify single-cell resolution or cell-type-resolved readouts; the abstract does not specify which altered transcripts are direct versus indirect ZFHX3 targets; the abstract does not specify sequencing depth, sampling times, or analysis pipeline details.
Source:
The web research summary mentions single-cell RNA-seq as a higher-resolution comparator in related human skin studies, but this paper itself reports bulk RNA sequencing.
Ranked Citations
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Extracted from this source document.
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