Source 1primary paper2025MED
Toolkit/SOSHI-seq
SOSHI-seq
Also known as: Screening of Self-transcribed Hormone Inducible response elements coupled to sequencing
Taxonomy: Technique Branch / Method. Workflows sit above the mechanism and technique branches rather than replacing them.
Summary
We present a cheap, rapid, and versatile assay called SOSHI-seq (Screening of Self-transcribed Hormone Inducible response elements coupled to sequencing).
Usefulness & Problems
Why this is useful
SOSHI-seq is a sequencing-based functional assay for testing whether putative DNA response elements can act as hormone-response elements. The abstract states that it can assay thousands of synthetic DNA sequences.; high-throughput functional testing of putative nuclear hormone receptor response elements; testing thousands of synthetic DNA sequences for hormone-response element activity; complementing ChIP-Seq analysis to identify functional occupied response elements at genome-wide scale
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SOSHI-seq is a sequencing-based functional assay for testing whether putative DNA response elements can act as hormone-response elements. The abstract states that it can assay thousands of synthetic DNA sequences.
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high-throughput functional testing of putative nuclear hormone receptor response elements
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testing thousands of synthetic DNA sequences for hormone-response element activity
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complementing ChIP-Seq analysis to identify functional occupied response elements at genome-wide scale
Problem solved
It addresses the need to functionally test putative nuclear hormone receptor response elements at high throughput. The abstract also positions it as a complement to ChIP-Seq for identifying functional occupied elements.; provides a functional assay for putative response elements rather than occupancy-only identification
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It addresses the need to functionally test putative nuclear hormone receptor response elements at high throughput. The abstract also positions it as a complement to ChIP-Seq for identifying functional occupied elements.
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provides a functional assay for putative response elements rather than occupancy-only identification
Problem links
provides a functional assay for putative response elements rather than occupancy-only identification
LiteratureIt addresses the need to functionally test putative nuclear hormone receptor response elements at high throughput. The abstract also positions it as a complement to ChIP-Seq for identifying functional occupied elements.
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It addresses the need to functionally test putative nuclear hormone receptor response elements at high throughput. The abstract also positions it as a complement to ChIP-Seq for identifying functional occupied elements.
Published Workflows
Objective: Develop and apply a high-throughput sequencing-based assay to functionally test putative nuclear hormone receptor response elements and complement ChIP-Seq-based occupancy analysis.
Why it works: The abstract states that SOSHI-seq adapts STARR-seq to test thousands of synthetic DNA sequences for hormone-response element activity, enabling functional readout that complements chromatin occupancy information from ChIP-Seq.
hormone-response element activitynuclear receptor-dependent functional occupancy in chromatinSTARR-seq adaptationsequencing-based screeningcomplementary use with ChIP-Seq
Stages
- 1.Synthetic response-element library testing(broad_screen)
This stage provides high-throughput functional testing across many candidate synthetic sequences.
Selection: capacity of thousands of synthetic DNA sequences to act as hormone-response elements
- 2.Comparison with ChIP-Seq occupancy analysis(confirmatory_validation)
The abstract states SOSHI-seq is a suitable complement to ChIP-Seq analysis, indicating a downstream interpretive stage that combines functional assay output with chromatin occupancy information.
Selection: identify functional response elements occupied by nuclear receptors in chromatin
Taxonomy & Function
Primary hierarchy
Technique Branch
Method: A concrete measurement method used to characterize an engineered system.
Mechanisms
selection/enrichment coupled to sequencingself-transcribing reporter-based functional readoutTarget processes
recombinationselectionImplementation Constraints
cofactor dependency: cofactor requirement unknownencoding mode: genetically encodedimplementation constraint: context specific validationoperating role: sensor
The assay requires synthetic DNA sequences and sequencing readout. The abstract also states that the protocol is adapted from STARR-seq.; requires synthetic DNA sequence libraries; requires sequencing-based readout; is described as an adaptation of STARR-seq
The abstract does not show that SOSHI-seq alone measures chromatin occupancy in native chromatin. Instead, it is presented as complementary to ChIP-Seq.; demonstration in the abstract is specifically described using thyroid hormone nuclear receptors as the example
Validation
Cell-freeBacteriaMammalianMouseHumanTherapeuticIndep. Replication
Supporting Sources
Ranked Claims
Using thyroid hormone nuclear receptors as an example, SOSHI-seq is a suitable complement to ChIP-Seq analysis for identifying at genome-wide scale the functional response elements occupied by nuclear receptors in chromatin.
analysis scale genome-wide
SOSHI-seq allows testing the capacity of thousands of synthetic DNA sequences to act as hormone-response elements.
sequence count scale thousands
SOSHI-seq is an adaptation of the STARR-seq method.
SOSHI-seq is a cheap, rapid, and versatile assay.
Approval Evidence
1 source4 linked approval claimsfirst-pass slug soshi-seq
We present a cheap, rapid, and versatile assay called SOSHI-seq (Screening of Self-transcribed Hormone Inducible response elements coupled to sequencing).
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application scopesupports
Using thyroid hormone nuclear receptors as an example, SOSHI-seq is a suitable complement to ChIP-Seq analysis for identifying at genome-wide scale the functional response elements occupied by nuclear receptors in chromatin.
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assay capabilitysupports
SOSHI-seq allows testing the capacity of thousands of synthetic DNA sequences to act as hormone-response elements.
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method lineagesupports
SOSHI-seq is an adaptation of the STARR-seq method.
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tool descriptionsupports
SOSHI-seq is a cheap, rapid, and versatile assay.
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Comparisons
Source-stated alternatives
The abstract explicitly contrasts SOSHI-seq with ChIP-Seq as a complementary method and states that it is adapted from STARR-seq.
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The abstract explicitly contrasts SOSHI-seq with ChIP-Seq as a complementary method and states that it is adapted from STARR-seq.
Source-backed strengths
cheap; rapid; versatile; high-throughput
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cheap
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rapid
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versatile
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high-throughput
Compared with chromatin immunoprecipitation
The abstract explicitly contrasts SOSHI-seq with ChIP-Seq as a complementary method and states that it is adapted from STARR-seq.
Shared frame: source-stated alternative in extracted literature
Strengths here: cheap; rapid; versatile.
Relative tradeoffs: demonstration in the abstract is specifically described using thyroid hormone nuclear receptors as the example.
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The abstract explicitly contrasts SOSHI-seq with ChIP-Seq as a complementary method and states that it is adapted from STARR-seq.
Compared with chromatin immunoprecipitation sequencing
The abstract explicitly contrasts SOSHI-seq with ChIP-Seq as a complementary method and states that it is adapted from STARR-seq.
Shared frame: source-stated alternative in extracted literature
Strengths here: cheap; rapid; versatile.
Relative tradeoffs: demonstration in the abstract is specifically described using thyroid hormone nuclear receptors as the example.
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The abstract explicitly contrasts SOSHI-seq with ChIP-Seq as a complementary method and states that it is adapted from STARR-seq.
Compared with STARR-seq
The abstract explicitly contrasts SOSHI-seq with ChIP-Seq as a complementary method and states that it is adapted from STARR-seq.
Shared frame: source-stated alternative in extracted literature
Strengths here: cheap; rapid; versatile.
Relative tradeoffs: demonstration in the abstract is specifically described using thyroid hormone nuclear receptors as the example.
Source:
The abstract explicitly contrasts SOSHI-seq with ChIP-Seq as a complementary method and states that it is adapted from STARR-seq.
Ranked Citations
- 1.