Data Repository Submission Quick Guides

Generalist repository for publishing research datasets (with DOIs and professional curation).

When to use Dryad

• No domain-specific repository (e.g., GEO/SRA/dbGaP) fits your data.
• You’re publishing raw and/or processed data underlying a manuscript (or meeting funder/journal requirements).
• You want FAIR sharing (findable, accessible, interoperable, reusable) with a persistent identifier and curation.

Step-by-Step Submission

1) Prepare your data

• Organize logically: folders, descriptive file names, consistent headers.
• Prefer open formats: CSV, TSV, TXT, XML, JSON (proprietary files accepted but less reusable).
• README & documentation: describe purpose, file structure, variable/abbreviation definitions; include protocols or supplementary docs.
• Restrictions: do not include PHI, confidential data, or sensitive species locations (unless permitted/redacted).
• Language: provide all content in English.

2) Timing your submission

• Submit before, during, or after manuscript submission; many journals integrate directly with Dryad.
• Embargoes: generally limited; data are released at article publication (special cases: dissertations, press embargoes).
• Private for Peer Review: generate a secure private link for editors/reviewers; release upon acceptance.

3) Login & authentication

• ORCID iD required for submitters (can register during submission).
• NC State SSO: NC State affiliates can link ORCID to their NC State credentials for simplified login. Learn more about ORCID at NC State

4) Describe your dataset (metadata)

• Title: clear, descriptive dataset title.
• Abstract: purpose, methods, scope; include key context for reuse.
• Contributors: authors and contributors (add ORCID iDs where available).
• Keywords: improve discoverability.
• Funding & acknowledgments: include grants (e.g., P30ES025128).
• Related works: link to associated publications, preprints, or software repositories.

5) Upload your files

• Sources: upload from computer or via URL (Google Drive links are not supported).
• Classify files: Data (raw/processed), Software (scripts/code/workflows), Supplemental Information (figures/tables/appendices).
• Tabular checks: CSV/TSV/XLS/XLSX (<50 MB) are automatically validated; fix flagged issues before finalizing.
• Large files: >10 GB per file are allowed but may increase handling/curation time.

6) Review & submit

• Verify metadata, contributors, affiliations, and grant acknowledgments.
• Data Publishing Charge (DPC): normally required by Dryad, but waived for NC State affiliates (see benefits below).
• Submit; Dryad performs professional curation and assigns a DOI upon publication.

Checklist

CHHE Notes

• Cite CHHE P30 (P30ES025128) and any other relevant grants in metadata/acknowledgments.
• If human-participant data are involved, confirm IRB and consider dbGaP (instead of or in addition to Dryad) before submitting.
• Questions on formats, licensing, or compliance? Contact CHHE Data Support.

Useful Links

• Dryad Submission Portal
• Official Dryad Submission Guide
• Good Data Practices – Dryad

Last updated: September 2025

GEO is an NCBI repository for functional genomics data (microarray and sequencing-based assays). This guide summarizes the two submission routes and key requirements for raw and processed data, including single-cell specifics.

When to use GEO

• Your project generated gene expression, epigenomics, or other functional genomics datasets.
• Your journal/funder requires a domain repository. GEO works with SRA for raw HTS reads and hosts processed/metadata files.
• You can keep the record private until publication and share reviewer access links.

Step-by-Step Submission

1) Choose the correct submission route

• High-throughput sequencing (HTS) (RNA-seq, miRNA-seq, ChIP-seq, ATAC-seq, RIP-seq, Hi-C, methyl-seq, bulk and single-cell): raw reads to SRA; processed data + metadata to GEO.
• Microarray & other non-HTS data: array raw files (e.g., CEL, IDAT), processed signal matrices, and metadata spreadsheets to GEO.
• Overview: GEO Submission page

2) Prepare your files (by data type)

HTS — Raw reads (to SRA)

• FASTQ files (paired reads as R1/R2; include index/barcode reads if applicable).
• File naming: unique, consistent sample identifiers; indicate lane/read (e.g., sampleA_S1_L001_R1.fastq.gz).
• Bulk vs. single-cell:
  • Bulk: submit demultiplexed per-sample FASTQs.
  • Single-cell (e.g., 10x Genomics, Drop-seq, inDrops): NCBI recommends keeping most data in the original multiplexed form when appropriate (retain index/cell barcodes). See HTS Raw data.
• Optional alignments: BAM/SAM files may be uploaded to SRA if desired, but they are not considered processed data for GEO display.
• Submit FASTQs via the SRA submission portal and record the assigned BioProject/SRA accessions to reference in your GEO metadata.
• Large file transfer: use NCBI’s FTP or Aspera-based methods for efficient uploads.

HTS — Processed data (to GEO)

• Expression/quantification tables (counts, TPM/FPKM). For single-cell, provide gene × cell matrices and related annotation files.
• Peak calling outputs for ChIP-seq/ATAC-seq (BED, narrowPeak/broadPeak), plus optional coverage tracks (bigWig/bedGraph).
• Methylation summaries (e.g., beta values, coverage tables).
• Note: alignment files (BAM/SAM) are not accepted as processed data for GEO records. See HTS Processed data.

Single-cell specifics

• Raw reads: retain multiplexing and index/cell barcodes when recommended (e.g., 10x/Drop-seq/inDrops); submit to SRA.
• Processed outputs: include the standard 10x-style trio when applicable:
  • matrix.mtx (sparse counts matrix)
  • barcodes.tsv (cell barcodes)
  • features.tsv (genes/features)
  Provide any additional cell/feature annotations (cluster IDs, metadata) used in downstream analyses.
• Document barcoding/UMI strategy, chemistry version, and demultiplexing in the README/methods.

Microarray & non-HTS

• Raw array files (e.g., CEL for Affymetrix, IDAT for Illumina) plus processed signal matrices.
• Platform annotations, sample-level metadata, and normalized result tables as required by GEO spreadsheets.

3) Complete metadata spreadsheets

• Download and complete the required Series and Sample spreadsheets:
  • HTS: HTS metadata
  • Microarray/non-HTS: Spreadsheet submission
• One spreadsheet per data type in your study (e.g., separate sheets for RNA-seq vs. ATAC-seq, if both are present).
• Include organism, tissue/cell type, treatment/condition, library strategy, platform, experimental design, and file associations (which samples map to which raw/processed files).
• If raw reads are already in SRA, include the corresponding BioProject/SRA accessions so GEO can link them.

4) Submit

• HTS: Submit raw FASTQs to SRA; upload processed files and spreadsheets to GEO. Ensure spreadsheets reference the correct SRA accessions.
• Microarray/non-HTS: Upload spreadsheets, raw array files (CEL/IDAT), processed matrices, and supporting docs to GEO.
• Expect a GSE series accession (and GSM sample accessions). Initial processing is typically a few business days.

5) Privacy & peer review

• Submissions can remain private until manuscript acceptance; generate reviewer access links for editors/referees.
• Upon release, GEO will display processed data/metadata and link to SRA raw reads.

Checklist

Useful Links

• GEO Submission Overview
• HTS Submission Guide (bulk & single-cell)
• HTS Metadata Requirements
• Microarray & Non-HTS Spreadsheet Submission
• SRA Submission Portal (raw FASTQ)

Last updated: October 2025