Cerebellar neurocan gene expression is a common pathogenic factor of trigeminal neuralgia and depression methods
Aim. Evidence-backed execution summary for Cerebellar neurocan gene expression is a common pathogenic factor of trigeminal neuralgia and depression methods from Cerebellar neurocan gene expression is a common pathogenic factor of trigeminal neuralgia and depression.
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This experiment, in seven questions
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rat
Subject model for the experiment.
- Use
- confirm full cohort details in the source paper
RNA extraction and RT-PCR verification of mRNA transcriptional level
reagent used in the protocol.
- Use
- Total RNA was extracted from cerebellar tissues ( n = 3 per group) using TRIzol reagent. cDNA was synthesized using a reverse transcription kit (Vazyme, Cat#R223). Quantitative PCR was performed with a SYBR Green kit (Vazyme, Cat#Q311-02) on a real-time PCR system. GAPDH served as the internal control,...
rs-fMRI data preprocessing and analysis
This study employed the GRETNA toolbox in Matlab 2020a and the ANTs software for the preprocessing of rs-fMRI data. The detailed procedures are outlined as follows: (1) removal of the first five volumes to mitigate potential instability; (2) time slice correction and head motion correction: subjects with head motion...
- Use
- This study employed the GRETNA toolbox in Matlab 2020a and the ANTs software for the preprocessing of rs-fMRI data. The detailed procedures are outlined as follows: (1) removal of the first five volumes to mitigate potential instability; (2) time slice correction and head motion correction: subjects with head motion...
Open field test
The open field test is a widely recognized and classical experimental method used to assess the emotional behavior of animals. The experimental apparatus consisted of a rectangular open box measuring 100 cm × 100 cm × 40 cm, with white walls and a black floor. All...
- Use
- The open field test is a widely recognized and classical experimental method used to assess the emotional behavior of animals. The experimental apparatus consisted of a rectangular open box measuring 100 cm × 100 cm × 40 cm, with white walls and a black floor. All...
Elevated plus maze test
The elevated plus maze (EPM) test is a well-established method for assessing emotional behavior in animals. The apparatus consisted of two enclosed arms (50 cm × 10 cm), two open arms (50 cm × 10 cm), and a central platform (10 cm × 10&...
- Use
- The elevated plus maze (EPM) test is a well-established method for assessing emotional behavior in animals. The apparatus consisted of two enclosed arms (50 cm × 10 cm), two open arms (50 cm × 10 cm), and a central platform (10 cm × 10&...
RNA extraction and RT-PCR verification of mRNA transcriptional level
Total RNA was extracted from cerebellar tissues ( n = 3 per group) using TRIzol reagent. cDNA was synthesized using a reverse transcription kit (Vazyme, Cat#R223). Quantitative PCR was performed with a SYBR Green kit (Vazyme, Cat#Q311-02) on a real-time PCR system. GAPDH served as the internal control,...
- Use
- Total RNA was extracted from cerebellar tissues ( n = 3 per group) using TRIzol reagent. cDNA was synthesized using a reverse transcription kit (Vazyme, Cat#R223). Quantitative PCR was performed with a SYBR Green kit (Vazyme, Cat#Q311-02) on a real-time PCR system. GAPDH served as the internal control,...
Discussion
However, this study still has several limitations that warrant acknowledgment. Firstly, the whole genome data source used in this study is relatively homogeneous, being derived exclusively from the European population. Given the heterogeneity of patient populations, future studies should incorporate large-scale, mul...
- Use
- However, this study still has several limitations that warrant acknowledgment. Firstly, the whole genome data source used in this study is relatively homogeneous, being derived exclusively from the European population. Given the heterogeneity of patient populations, future studies should incorporate large-scale, mul...
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Open quote workflowStep-by-step procedure
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Open field test
The open field test is a widely recognized and classical experimental method used to assess the emotional behavior of animals. The experimental apparatus consisted of a rectangular open box measuring 100 cm × 100 cm × 40 cm, with white walls and a black floor. All animals were assessed on the 28 th day post-surgery. The experiment was performed in a quiet setting with dim lighting. Before the experiment, the rats were placed in the behavioral laboratory for one hour for adaptation. Each rat was gently placed in the central area of the open box and allowed to move freely for 5 min. Key observation indicators included total movement distance and movement speed. Following each trial, the box was promptly cleaned with low-concentration alcohol. Subsequent trials commenced only after the alcohol had fully evaporated.
Elevated plus maze test
The elevated plus maze (EPM) test is a well-established method for assessing emotional behavior in animals. The apparatus consisted of two enclosed arms (50 cm × 10 cm), two open arms (50 cm × 10 cm), and a central platform (10 cm × 10 cm). The entire apparatus was elevated 50 cm above the ground. Measurements were conducted on the 28 th day post-surgery for both the Sham and TN groups. Rats were placed in the center of the maze facing the open arms. Using animal behavior analysis software, the number of entries into the open arms and the duration of time spent in the open arms within a 5-minute period were recorded. Subsequently, the percentages of time spent in the open arms were calculated. The primary observation index was the percentage of time spent in the open arms, which served as an i...
Functional network properties analysis
This study employed the GRETNA toolbox and graph theory methods to systematically analyze the characteristics of brain network. Separate comparisons were conducted for the two patient groups, TN and depression, each against their own healthy controls. To investigate the variations in graph theory features across sparsity levels, this study computed the properties of brain regions exhibiting significant differences across a sparsity threshold range of 0.1-0.5 (step = 0.01) for the TN dataset and 0.1-0.48 (step = 0.01) for the depression dataset. Notably, the graph theory features of the TN group and the depression group demonstrated σ (σ > 1) throughout the entire connectivity density interval, with statistically significant differences. Futhermore, the analysis conducted using the NBS approach revealed no significant FC alterna...
Measurement outputs
What raw and processed outputs should exist?
In this study, neuroimaging data were integrated with whole-genome sequencing data to identify common genetic risk factors. Initially, single nucleotide polymorphisms (SNPs) ass...
- Raw artifact
- Field or section images captured from matched samples
- Processed artifact
- Selected representative panels with quantified intensity, counts, or area measurements
- Reported as
- Per-group imaging summaries with representative figures and quantified endpoints
For TN, the genotyping and phenotype data were obtained from the UK Biobank. We included 508 clinically confirmed cases (ICD-10 code: G50.0) and 2,540 matched controls without n...
- Raw artifact
- Per-sample or per-animal endpoint measurements collected during the experiment
- Processed artifact
- Structured table with cleaned measurements ready for comparison
- Reported as
- Summary statistics and between-group or across-timepoint comparisons
For depression, we obtained publicly available GWAS summary statistics released by the Psychiatric Genomics Consortium (PGC) [ ]. This dataset is based on a meta-analysis of thr...
- Raw artifact
- Per-sample or per-animal endpoint measurements collected during the experiment
- Processed artifact
- Structured table with cleaned measurements ready for comparison
- Reported as
- Summary statistics and between-group or across-timepoint comparisons
This study utilized the S-PrediXcan method within the framework of whole-transcriptome association analysis and SMR to identify trait-associated genetic regulatory gene expressi...
- Raw artifact
- Per-sample or per-animal endpoint measurements collected during the experiment
- Processed artifact
- Structured table with cleaned measurements ready for comparison
- Reported as
- Summary statistics and between-group or across-timepoint comparisons
Analysis plan
How should the outputs become interpretable results?
Acquisition
Collect raw experimental outputs with enough metadata to preserve sample identity, condition, and timing.
inferred from protocolPreprocessing / cleaning
For depression, we obtained publicly available GWAS summary statistics released by the Psychiatric Genomics Consortium (PGC) [ ].
from paperScoring or quantification
Quantify the primary readouts for this experiment: In this study, neuroimaging data were integrated with whole-genome sequencing data to identify common genetic risk factors. Initially, single nucleotide polymorphisms (SNPs) ass...; For TN, the genotyping and phenotype data were obtained from the UK Biobank. We included 508 clinically confirmed cases (ICD-10 code: G50.0) and 2,540 matched controls without n...; For depression, we obtained publicly available GWAS summary statistics released by the Psychiatric Genomics Consortium (PGC) [ ]. This dataset is based on a meta-analysis of thr...; This study utilized the S-PrediXcan method within the framework of whole-transcriptome association analysis and SMR to identify trait-associated genetic regulatory gene expressi....
from paperStatistical comparison
For depression, we obtained publicly available GWAS summary statistics released by the Psychiatric Genomics Consortium (PGC) [ ]. This dataset is based on a meta-analysis of thr...; S-PrediXcan is a transcriptome-wide association analysis method that leverages summary statistics. It aims to identify genes associated with complex traits or diseases by integr...; SMR is a Mendelian randomization method that leverages summary data, enabling the utilization of GWAS summary statistics for causal inference. The central objective is to deduce...; The primary analyses consisted of two sequential steps. First, we performed a series of two-sample bidirectional MR analysis. When TN was modeled as the exposure, genetically pr...
from paperReporting output
Report representative outputs alongside summary comparisons for In this study, neuroimaging data were integrated with whole-genome sequencing data to identify common genetic risk factors. Initially, single nucleotide polymorphisms (SNPs) ass..., For TN, the genotyping and phenotype data were obtained from the UK Biobank. We included 508 clinically confirmed cases (ICD-10 code: G50.0) and 2,540 matched controls without n..., For depression, we obtained publicly available GWAS summary statistics released by the Psychiatric Genomics Consortium (PGC) [ ]. This dataset is based on a meta-analysis of thr..., This study utilized the S-PrediXcan method within the framework of whole-transcriptome association analysis and SMR to identify trait-associated genetic regulatory gene expressi....
inferred from protocolStructured statistical methods
For depression, we obtained publicly available GWAS summary statistics released by the Psychiatric Genomics Consortium (PGC) [ ]. This dataset is based on a meta-analysis of thr...; S-PrediXcan is a transcriptome-wide association analysis method that leverages summary statistics. It aims to identify genes associated with complex traits or diseases by integr...; SMR is a Mendelian randomization method that leverages summary data, enabling the utilization of GWAS summary statistics for causal inference. The central objective is to deduce...; The primary analyses consisted of two sequential steps. First, we performed a series of two-sample bidirectional MR analysis. When TN was modeled as the exposure, genetically pr...
source structuredSource and audit
What supports the facts on this page?
Evidence quotes (3)
The open field test is a widely recognized and classical experimental method used to assess the emotional behavior of animals. The experimental apparatus consisted of a rectangular open box measuring 100 cm × 100 cm × 40 cm, with white walls and a black floor. All animals were assessed on the 28 th day post-surgery. The experiment was performed in a quiet setting with dim lighting. Before the experiment, the rats were placed in the behavioral laboratory for one hour for adaptation. Each rat was gently placed in the central area of the open box and allowed to move freely for 5 min. Key observation indicators included total movement distance and movement speed. Following each trial, the box was promptly cleaned with low-concentration alcohol. Subsequent trials commenced only after the alcohol had fully evaporated.
The elevated plus maze (EPM) test is a well-established method for assessing emotional behavior in animals. The apparatus consisted of two enclosed arms (50 cm × 10 cm), two open arms (50 cm × 10 cm), and a central platform (10 cm × 10 cm). The entire apparatus was elevated 50 cm above the ground. Measurements were conducted on the 28 th day post-surgery for both the Sham and TN groups. Rats were placed in the center of the maze facing the open arms. Using animal behavior analysis software, the number of entries into the open arms and the duration of time spent in the open arms within a 5-minute period were recorded. Subsequently, the percentages of time spent in the open arms were calculated. The primary observation index was the percentage of time spent in the open arms, which served as an indicator for evaluating depressive-like behavior. The device was cleaned with low-concentration alcohol, and thoroughly dried prior to the next experiment.
This study employed the GRETNA toolbox and graph theory methods to systematically analyze the characteristics of brain network. Separate comparisons were conducted for the two patient groups, TN and depression, each against their own healthy controls. To investigate the variations in graph theory features across sparsity levels, this study computed the properties of brain regions exhibiting significant differences across a sparsity threshold range of 0.1-0.5 (step = 0.01) for the TN dataset and 0.1-0.48 (step = 0.01) for the depression dataset. Notably, the graph theory features of the TN group and the depression group demonstrated σ (σ > 1) throughout the entire connectivity density interval, with statistically significant differences. Futhermore, the analysis conducted using the NBS approach revealed no significant FC alternations in either TN patients or depression patients compared to healthy controls.
Machine-readable layer
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