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Supplementary research data index listing spreadsheet files and variable definitions associated with epigenome-wide analyses of neuronal and glial nuclei from human prefrontal cortex samples in Parkinson’s disease cohorts stratified by GBA1 genetic status.
Document Type:
Supplementary data description
Content Type:
Data file index and variable definitions
Research Field:
Epigenetics; Neurodegenerative disease research
Disease Focus:
Parkinson’s disease
Biological Material:
Human prefrontal cortex nuclei samples
Cell Types:
NeuN+ neuronal nuclei; SOX10+ oligodendrocyte nuclei; double negative glial nuclei
Genetic Factor:
GBA1 variant status
Data Types:
Sample metadata; quality control metrics; cell composition estimates; differential DNA methylation results; gene ontology analysis
Analytical Methods:
EWAS (epigenome-wide association study); linear regression analysis; interaction models; Tukey HSD test; ANOVA; χ² test
Laboratory Methods:
EPIC DNA methylation array; bisulfite conversion; fluorescence-activated nuclei sorting (FANS)
Variables Included:
PD status; GBA1 status; sex; dementia status; Braak Lewy body stage; Braak neurofibrillary tangle stage; methylation signal intensity; principal components; genomic site coordinates
Sample Groups:
PD-GBA1; PD-non-GBA1; Control-GBA1; Control-non-GBA1
Brain Region:
Prefrontal cortex
Number of Supplementary Files:
14
File Formats:
XLS spreadsheets
Key Measurements:
DNA methylation beta values; cell composition fractions; quality control metrics; differential methylation statistics
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Year:
2025
Note:
Region / city
Topic:
Central nervous system tumor diagnostics
Document type:
Scientific article
Author:
Aldape K, Capper D, von Deimling A, Giannini C, Gilbert MR, Hawkins C, Hench J, Jacques TS, Jones D, Louis DN, Mueller S, Orr BA, Nasrallah M, Pfister SM, Sahm F, Snuderl M, Solomon D, Varlet P, Wesseling P
DOI:
10.1093/noajnl/vdae228
PMID:
39902391
PMCID:
PMC11788596
Context:
A scientific article offering guidelines on the use of DNA methylation profiling for diagnosing tumors in the central nervous system.
Year:
2017
Region / City:
Netherlands, Canada
Topic:
DNA Methylation Analysis
Document Type:
Research Supplementary Materials
Institution:
Not specified
Author:
Forest et al.
Target Audience:
Researchers in genomics and molecular biology
Period of validity:
Not specified
Date of approval:
Not specified
Date of changes:
Not specified
Document type:
Supplementary material
Subject:
Differential DNA methylation analysis
Keywords:
DNA methylation, DMPs, DMRs, CpG island, GO enrichment, KEGG pathway, polyps, normal tissue
Biological context:
Comparison between polyp and control tissue samples
Analytical methods:
Correlation heatmap, box plot normalization, differential methylation analysis, GO and KEGG enrichment analysis
Genes mentioned:
LPA, SVIL, KRT18, MYH13 and others listed in enrichment tables
Statistical measures:
Pearson’s correlation coefficient, T value, pvalue, adjusted pvalue, qvalue
Biological processes highlighted:
Regulation of membrane potential, axon guidance, extracellular matrix organization, ion transmembrane transport
Abbreviations:
TSS (transcription start site), P (polyp), C (control), FEM (Functional epigenetic modules), DMP (differentially methylated position), DMR (differentially methylated region)
Year:
2022
Region / city:
Global
Theme:
DNA methylation analysis
Document type:
Product datasheet
Organization / institution:
Abcam
Author:
Abcam
Target audience:
Researchers in molecular biology, genetics, and biochemistry
Validity period:
Not specified
Approval date:
21 June 2022
Modification date:
Not specified
Year:
2026
Institution:
Johns Hopkins Hospital, Asan Medical Center
Study Type:
Molecular biology study
Methods:
Droplet digital PCR, MSP, bisulfite sequencing, ddQMSP, mRNA expression analysis
Biomarkers:
SOX17, ACTB, KRAS, GNAS, seven marker genes
Sample Type:
Surgically aspirated pancreatic cyst fluid, pancreatic cell lines, normal pancreatic tissue
Sample Size:
183 patients (discovery and validation sets)
Pathology:
IPMN, MCN, SCN, HGD, INV, IGD, LGD
Data Presentation:
1-D ddPCR plots, heat maps, AUC values, box plots, correlation plots
Statistical Measures:
Mean ± standard deviation, coefficient of determination (R²), coefficient of variation (% CV), 95% confidence interval
Experimental Conditions:
5-Aza-2′-deoxycytidine, trichostatin A treatment
Comparisons:
Between hospitals (JHH vs AMC), among cyst types, stratified by mutation status and histologic grade
Year:
2025
Region / city:
China
Subject:
Nasopharyngeal carcinoma, RNA modification
Document type:
Original research article
Institution:
University hospital, Otolaryngology department
Author:
Not specified
Target audience:
Researchers, clinicians
Period of validity:
Not specified
Approval date:
Not specified
Date of revisions:
Not specified
Year:
2026
Region / City:
Not specified
Subject:
TP53 mutations, DNA methylation, GC patients
Document Type:
Supplementary material
Institution:
Not specified
Author:
Not specified
Target Audience:
Researchers and clinicians in molecular genetics and oncology
Methods:
Sanger sequencing, pyrosequencing, primer design
Data Source:
Patient tumor samples
Genomic Reference:
GRCh37: Genome Reference Consortium human build 37
Figures Included:
Methylation distribution and survival analysis
Tables Included:
Primer sequences, TP53 mutations
Clinical Context:
Neoadjuvant and adjuvant chemotherapy subgroups
Year:
Not specified
Region / City:
Not specified
Subject:
DNA methylation, LRP11, HCC
Document Type:
Supplementary figure
Organization / Institution:
SMART database
Author:
Not specified
Target Audience:
Researchers in genomics
Effective Period:
Not specified
Approval Date:
Not specified
Date of Changes:
Not specified
Year:
2026
Study Population:
Whites
Sample Type:
Plasma, Urine
Disease Focus:
Cancer
Number of Cancer Cases:
41
Number of Control Cases:
11
Genes Analyzed:
CDO1, TAC1, HOXA7, HOXA9, SOX17, ZFP42
Parameters Measured:
Sensitivity, Specificity, Positive Predictive Value (PPV), Negative Predictive Value (NPV), Area Under the Curve (AUC), 95% Confidence Interval
Data Presentation:
Tabular
Cutoff Criteria:
Detectable vs. Non-detectable
Combined Analysis:
At least 3 positive genes
Year:
2023
Region / City:
Denmark
Theme:
Cervical Cancer Screening, HPV Testing, DNA Methylation
Document Type:
Research Article
Organization / Institution:
University Research Clinic for Cancer Screening, Aarhus University
Authors:
Mette Tranberg, Severien Van Keer, Albertus T Hesselink, Pia Nørgaard, Rikke Brøndum, Chunsen WU, Line Winther Gustafson, Anne Hammer, Pinar Bor, Karen Omann Binderup, Christina Blach, Alex Vorsters, Renske Steenbergen
Target Audience:
Researchers, Healthcare Professionals, Medical Community
Period of Application:
Not specified
Approval Date:
Not specified
Date of Changes:
Not specified
Study Registration:
Clinicaltrials.gov: NCT05065853
Keywords:
DNA methylation, cervical cancer screening, HPV DNA testing, urinary HPV testing, early detection of cancer/methods
Abstract:
The study evaluates the performance of ASCL1/LHX8 DNA methylation markers and HPV genotyping in first-void urine samples for detecting high-grade cervical intraepithelial neoplasia (CIN2+) and cervical cancer in HPV-positive women, comparing it with clinician-collected cervical samples.
Year:
2026
Institution:
Nova Southeastern University, Ft. Lauderdale
Course:
Neuromuscular Systems II
Credits:
2
Duration:
12 weeks, first semester of third year
Contributors:
Suzana Simoes PT, DPT, NCS; Kim B. Smith PT, DPT; Jennifer Canbek, PT, PhD, NCS
Target audience:
Physical therapy students
Activity type:
Laboratory learning activity with volunteer patients
Focus:
Clinical decision making using ICF model for Parkinson’s disease
Learning objectives:
Assessment of PD cases, development of PT problem list, formulation of patient-centered plan of care, implementation of treatment interventions, evaluation of treatment outcomes
Materials:
Assigned readings from Schenkman & McCulloch (2002), Schenkman et al. (2010)
Methods:
Lab sessions with patient volunteers, outcome measures, treatment sessions, video documentation, SOAP note assignments
Assessment:
Rubric-based evaluation of outcome measures, ICF model application, problem list, plan of care, goals, treatment, and documentation
Year:
Not specified
Region / city:
Not specified
Theme:
Parkinson’s disease, therapeutic research
Document Type:
Pre-Clinical Proposal Template
Organization / Institution:
Michael J. Fox Foundation
Author:
Not specified
Period of validity:
Not specified
Approval Date:
Not specified
Modification Date:
Not specified
FREEZING OF GAIT (FOG) IN PARKINSON’S DISEASE RESEARCH PROGRAM Request for Applications Pre-Proposal
Note:
Year
Document type:
Research Program Request for Applications
Organization / institution:
MJFF
Target audience:
Researchers, clinicians, industry partners
Year:
2023
Region / city:
Cardiff, Blackwood
Topic:
Dance for Parkinson’s
Document Type:
Case Study
Organization / institution:
English National Ballet, National Dance Company Wales
Author:
University of Roehampton
Target Audience:
People living with Parkinson’s, healthcare professionals, dance enthusiasts
Duration:
Ongoing
Approval Date:
2011
Revision Date:
Not specified
Year:
2023
Region / City:
Canberra
Document Type:
Medical procedure
Organization:
Canberra Health Services
Author:
Not specified
Target Audience:
Medical professionals, including Neurologists, Geriatricians, Nurses, Pharmacists, and Students under supervision
Period of Validity:
Not specified
Approval Date:
Not specified
Date of Modifications:
Not specified
Year:
2025
Region / city:
NENC
Document type:
Shared Care Protocol
Organization / institution:
NHS
Author:
NENC
Target audience:
NHS healthcare professionals
Period of validity:
Until December 2026
Approval date:
19th May 2025
Date of changes:
12th December 2024
Planned review date:
December 2026
Year:
Not specified
Region / city:
Not specified
Document Type:
Request for Applications
Organization / institution:
Not specified
Author:
Not specified
Target audience:
Researchers in Parkinson’s disease therapeutics
Period of validity:
Not specified
Approval date:
Not specified
Amendment date:
Not specified
Note:
Year
Document Type:
Research Proposal
Target Audience:
Researchers, Clinicians
Note:
Year
Topic:
Neurology, Parkinson’s Disease
Document Type:
Request for Applications
Year:
2018
Region / city:
London
Theme:
Dementia care, pharmacology
Document type:
Clinical guideline
Organization / institution:
London Dementia Clinical Network (NHS England and Improvement London Region)
Author:
Delia Bishara (Consultant Pharmacist, South London and Maudsley NHS Foundation Trust)
Target audience:
Healthcare professionals involved in dementia care
Effective period:
2018–present
Approval date:
Not specified
Date of amendments:
Not specified