A harmonized post-mortem neurodegeneration brain and spinal cord transcriptome compendium (ALS, FTD spectrum, Alzheimer's disease and others)
Study Design & Technical Specifications
Sample Size / Cohort
2 Data Files
Subject / Study Model
CNS Experimental / Clinical Model
Analytical Modalities
Primary Abstract & Repository Description
Source: Zenodo (CERN Open Data)Editorial Critique, Methodological Value & Reusability Guide
1. Scientific Context & Premise
Primary Premise (Zenodo (CERN Open Data)): "A harmonized post-mortem neurodegeneration brain and spinal cord transcriptome compendium (ALS, FTD spectrum, Alzheimer's disease and others)." Within Frontotemporal Dementia (FTD), this work examines Zenodo, Open Dataset, amyotrophic lateral sclerosis, frontotemporal dementia, Alzheimer's disease in relation to GRN, MAPT, and C9orf72 mutations, frontotemporal cortical thickness, and plasma NfL. Authored by Gibson, Christopher G., Jack, Alyssa, Gibson, Joseph.
2. Study Architecture & Findings
Study Architecture: Experimental / Clinical CNS Design (2 Data Files) utilizing RNA-seq [DOI: 10.5281/zenodo.23510663]. Reported quantitative parameters in the abstract include: 1847 samples. Key reported conclusion: "All exclusions and method deviations are listed in EXCLUSIONS_AND_DEVIATIONS.md."
3. Secondary Analysis & Reusability
Secondary Analysis Applications: (1) Cross-referencing RNA-seq variables (Zenodo, Open Dataset, amyotrophic lateral sclerosis, frontotemporal dementia, Alzheimer's disease) against open repositories in Frontotemporal Dementia (FTD); (2) Benchmarking feature distributions and effect sizes reported in "A harmonized post-mortem neurodegeneration brain and spinal cord transcriptome c"; (3) Informing cohort stratification and endpoint selection.
4. Methodological Caveats & Governance
Methodological Note: When integrating these RNA-seq findings, account for cohort-specific inclusion criteria (2 Data Files), potential site/instrument batch effects, and repository license terms (CC-BY-4.0).
Data Access, Reproducibility & Analysis Starter Guide
FAIR Open Science & Clinical Metadata Verification Protocol
Quick Data Access & Structured Export
Open the primary repository directly or download structured metadata (JSON / CSV) in one click.
This resource is indexed under FAIR (Findable, Accessible, Interoperable, and Reusable) open-science metadata standards, enabling programmatic cross-referencing across Europe PMC, Semantic Scholar, ClinicalTrials.gov, and CNS Open Data.
Programmatic Data Retrieval (Python Starter Code & Recommended SDKs)
Python Quickstart: Query Europe PMC & Semantic Scholar Metadata
# Fetch structured bibliographic & open-access data via Europe PMC REST API
import urllib.request
import urllib.parse
import json
query = "DOI:\"10.5281/zenodo.23510663\""
url = f"https://www.ebi.ac.uk/europepmc/webservices/rest/search?query={urllib.parse.quote(query)}&format=json&resultType=core"
with urllib.request.urlopen(url, timeout=10) as response:
payload = json.loads(response.read().decode("utf-8"))
results = payload.get("resultList", {}).get("result", [])
if results:
record = results[0]
print("Title:", record.get("title"))
print("Journal / Source:", record.get("journalTitle") or record.get("bookOrReportDetails"))
print("Cited By Count:", record.get("citedByCount", 0))Standardized 4-Step Workflow & Governance Checklist
Standardized Acquisition & Preprocessing Workflow
1. Programmatic Metadata & Full-Text OA Retrieval
Query Europe PMC or Crossref REST APIs using the persistent DOI/URL to retrieve structured XML full text, supplementary tables, and grant links.
2. Study Design & Cohort Eligibility Screening
Extract sample size, inclusion/exclusion criteria, and primary outcome endpoints for systematic review (PRISMA) inclusion.
3. Data Availability & Supplementary Repository Linkage
Locate accession numbers (GEO, SRA, OpenNeuro, DANDI, Zenodo, Figshare) referenced in the Data Availability section.
4. Citation Graph & Replication Tracking
Monitor supporting and contrasting citations over time to verify whether key findings have been independently replicated.
Reproducibility & Governance Checklist
- Verify whether the source is a peer-reviewed journal publication or an unrefereed preprint before clinical citation.
- Check supplementary data licenses (CC-BY / CC0) when extracting figures or summary statistics for meta-analyses.
- Cross-reference NCT clinical trial identifiers when evaluating therapeutic efficacy or biomarker endpoints.
Tags & Modalities
Related Frontotemporal Dementia Research & Datasets
Explore All DatasetsRelated Data & Resources
Academic Research & Medical Information Disclaimer
This page provides structured scientific metadata, methodological critiques, and open-data reusability guidelines intended strictly for neuroscience researchers and data scientists. It does not constitute medical advice, clinical diagnosis, or treatment recommendations.
Was this resource helpful?
Help improve data curation by sharing your feedback.