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Dataset Wiki Template

Below is a single generalized wiki template that works for both molecular/omics datasets (like Bru-seq/BruChase-seq + proteomics) and clinical studies/EAPs (like the ALL ALS Study). It’s modular: fill only the sections that apply.

Note: Not every section needs to be filled in as these are just a general guideline for how we fill wiki’s per dataset. Also contributors should feel free to stick to a format they are comfortable with as this is merely a guideline/suggestion.

Unified Study Wiki Template (Omics + Clinical)

Summary

Background: [Disease/condition + key biology/clinical problem].
Gap: [What is unknown / unmet need].
Study type & approach: This study [observational / interventional / expanded access / RCT / mechanistic / multi-omic] used [assays / intervention] in [participants/samples/models] to evaluate [primary concept: mechanism, biomarker, efficacy, safety, RNA stability, etc.].
Key findings: [2–5 bullets in sentence form: directionality, magnitude if known, comparisons].
Impact / utility: Data and [biospecimens / omics outputs] are available for the community to support [validation, meta-analysis, biomarker discovery, mechanism, etc.].

Overall Design

Study category: [Preclinical / translational / clinical; data-generating / therapeutic / access protocol].
Setting: [single-site / multicenter; countries; sites n= ].
Population / models:

  • Humans: [diagnosis criteria, subtypes, genotype groups, eligibility constraints]

  • Biospecimens: [serum/CSF/PBMC/fibroblasts/iPSC/post-mortem tissue; collection schedule]

  • Model systems (if any): [cell lines, iPSC-derived cells, animal models]

Arms / cohorts:

  • Cohort 1: [definition]

  • Cohort 2: [definition]

  • Controls: [healthy, disease, historical, matched, isogenic, etc.]

Exposure / intervention / perturbation (if applicable):

  • Agent: [drug/device/genetic manipulation]

  • Route & schedule: [e.g., IV weekly]

  • Duration: [e.g., 24 weeks]

  • Concomitant constraints: [trial-ineligible, washout, etc.]

Timepoints: [baseline; follow-up weeks; harvest points; chase times; post-mortem, etc.]
Replicates / sample size: [n participants; n biospecimens; biological/technical replicates]

Primary outcomes / endpoints:

  • Clinical: [ALSFRS-R, SVC, survival, QoL, safety/tolerability]

  • Biomarkers: [NfL, imaging, lab markers]

  • Molecular readouts: [RNA synthesis/stability, proteomics, mitochondrial/ribosomal transcripts]

Comparators: [placebo/active; baseline; historical controls; matched cohort; isogenic control; overexpression vs control].
Data sharing: [where datasets live; what’s shared: raw, processed, banked samples].

Data Types and Outputs

Generated datasets:

  • [RNA-seq / Bru-seq / BruChase-seq / proteomics / clinical phenotypes / biomarker assays]
    Key derived outputs:

  • [differential expression, RNA stability metrics, pathway enrichment, longitudinal trajectories, survival curves]
    File formats: [FASTQ, mzML, CSV, REDCap export, etc.] (optional)

Participant / Sample Details

Inclusion criteria: [diagnosis, age range, trial eligibility, disease stage].
Exclusion criteria: [key exclusions].
Demographics captured: [age, sex, race/ethnicity if available, site].
Clinical metadata captured: [onset type, duration, meds, ventilation status].
Sample metadata captured: [collection timepoint, processing protocol, batch, passage].

Methods

Clinical Procedures (if applicable)

  • Assessments: [ALSFRS-R schedule, respiratory measures, QoL instruments]

  • Safety monitoring: [AEs/SAEs, labs, infusion reactions]

  • Biospecimen collection: [serum/CSF schedule; storage/banking]

  • Remote procedures: [home infusions, tele-visits] (if applicable)

Molecular / Omics (if applicable)

  • Assays: [Bru-seq, BruChase-seq, proteomics, etc.]

  • Processing: [library prep, MS pipeline]

  • QC: [batch handling, outlier criteria]

  • Analysis: [models, thresholds, FDR; longitudinal modeling; survival analysis]

Key Findings (recommended bullets)

  • Finding 1: [What changed / what was observed + in what group].

  • Finding 2: [Comparator + direction].

  • Finding 3: [Mechanistic/functional link OR clinical interpretation].

  • Finding 4 (optional): [Null result statement if important—e.g., “no significant benefit vs historical controls”].

Limitations (optional but useful)

  • [open-label, non-randomized, historical controls, sample size, tissue availability, etc.]

Data Access and Reuse Notes

Where to access: [repository name + accession/identifier].
What’s available: [clinical + biomarker tables, processed omics matrices, raw files, banked serum].
Reuse suggestions: [meta-analysis, biomarker validation, mechanism studies, subgroup analyses].
Governance: [DUA/IRB limitations if any] (optional)

Contact

[Name, degree] — [institution]
Email: [email]
(Add center/program contact if relevant.)

Contributors

[List of contributors, optionally grouped by role: clinical sites, data generation, analysis, oversight.]

Publications

  • [Full citation]
    DOI: [doi]
    PMID: [pmid] (optional)

  • [Modality] deposited to [repository] under [identifier].
    (Example: proteomics in PRIDE / ProteomeXchange; imaging in OpenNeuro; etc.)

Keywords

[Condition, intervention, biomarker, assay type, cohort type, key pathways]