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
Need tighter control over gene expression timing or amplitude
DerivedRNA sequencing (RNA-seq) is a transcriptomic assay method used to measure gene-expression changes by sequencing RNA-derived libraries. In the cited study, it was applied to adult rat amygdala tissue and detected subtle expression changes associated with development, cellular function, and nervous system disease after gestational high-THC cannabis smoke exposure.
Taxonomy & Function
Primary hierarchy
Technique Branch
Method: A concrete measurement method used to characterize an engineered system.
Mechanisms
rna-derived sequencing-based transcript quantificationrna-derived sequencing-based transcript quantificationTechniques
Functional AssayFunctional AssaySelection / EnrichmentSequence VerificationSequence VerificationTarget processes
recombinationselectiontranscriptionInput: Light
Implementation Constraints
application domain: comparative transcriptomicsassay readout: gene expressionassay scope: time-series transcriptomicsassay scope: transcriptome-widecofactor dependency: cofactor requirement unknownencoding mode: genetically encodedimplementation constraint: context specific validationimplementation constraint: spectral hardware requirementmethod role: discoverymodality: transcriptomic profilingoperating role: builderoperating role: sensororganism: Cucumis sativussample type: ear skinsex subset reported: male subsetthroughput: hightimepoints reported: 6tissue: adult amygdala
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
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
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.
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.
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.
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-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 Affymetrix ATH1 microarray
RNA sequencing and Affymetrix ATH1 microarray address a similar problem space because they share transcription.
Shared frame: same top-level item type; shared target processes: transcription
Strengths here: looks easier to implement in practice.
Compared with Iris
RNA sequencing and Iris address a similar problem space because they share transcription.
Shared frame: same top-level item type; shared target processes: transcription
Relative tradeoffs: appears more independently replicated.
Compared with qRT-PCR
RNA sequencing and qRT-PCR address a similar problem space because they share transcription.
Shared frame: same top-level item type; shared target processes: transcription
Strengths here: looks easier to implement in practice.
Ranked Citations
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Extracted from this source document.
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