SPARC/dbGaP Quick-Reference
Under the NIH Genomic Data Sharing (GDS) Policy, read-level human genomic data must be deposited in a controlled-access repository such as dbGaP. If data does not require controlled access, it can be deposited in SPARC. Responsibility for regulatory compliance remains with the data submitter and Principal Investigator.
This information is provided for general demonstration purposes and is not a substitute for regulatory guidance. Ultimate responsibility for compliance with all applicable mandates — including the NIH Genomic Data Sharing Policy — rests solely with the investigator and Principal Investigator.
Table 1. SPARC and dbGaP Repositories at a Glance
| SPARC — Open-access repository | dbGaP — Controlled-access repository |
| Pennsieve / sparc.science Non-identifying derived data, metadata, code, protocols | NIH GDS Policy Human read-level, alignment, variant, and phenotype data |
Table 2. Deposit in SPARC
Open-access · Derived, processed, and non-identifying data
| Data category | Examples / content | Typical files / extensions |
|---|---|---|
| Derived / processed transcriptomics (bulk RNA-seq) | Gene expression summaries (non-identifying) | counts.tsv / .csvtpm.tsv / .csvDEG_results.tsv / .csvGSEA / GO / KEGG_results.tsv / .csv |
| Derived / processed single-cell & single-nucleus RNA-seq | Cell × gene matrices, cell-type labels, marker genes | matrix.mtx(.gz)features.tsv(.gz)barcodes.tsv(.gz)*_feature_bc_matrix.h5cell_annotations.csvmarkers.csv |
| Derived ATAC / accessibility outputs | Peaks and summarized accessibility | peaks.bedpeak_matrix.mtx / .h5motif_enrichment.tsvsummary plots ( .pdf / .png) |
| Visium spatial (Space Ranger summaries) | Spot × gene matrices + spatial metadata | filtered_feature_bc_matrix/*raw_feature_bc_matrix/*spatial/scalefactors_json.jsontissue_positions*.csv.cloupeweb_summary.html |
| Xenium summaries | Cell × gene matrices, segmentations, QC, de-identified images | cell_feature_matrix/* (MEX/H5/Zarr)cell_boundaries.parquetnucleus_boundaries.parquetQC html / csv de-ID images (PNG / TIFF / OME-TIFF / JP2) |
| QC reports (no reads) | Pipeline summaries and metrics | web_summary.htmlmetrics_summary.csvmultiqc_report.htmlQC reports ( .pdf) |
| Analysis code & workflows | Reproducibility artifacts | .R / .py / .ipynbDockerfileenvironment.yml / requirements.txtworkflow configs ( .yaml / .json) |
| Non-genomic modalities (de-identified) | Imaging, histology, microscopy; physiology / ephys | See SPARC accepted file formats |
| Documentation | Methods, protocols, README, crosswalk | README.mdprotocol docs ( .docx / .pdf)SDS metadata files |
Table 3. Deposit in dbGaP
Controlled-access · Human read-level, alignment, variant, and phenotype data
| Data category | Examples / content | Typical files / extensions |
|---|---|---|
| Read-level sequencing | Raw reads + base quality scores | *.fastq / .fq / .fastq.gz / .fq.gzBCL run folders |
| Alignments / near-raw | Aligned or unaligned reads | *.bam + index (.bai / .csi)*.cram + index (.crai)uBAM (unaligned .bam) |
| Variants | Genotype / variant calls | *.vcf / .vcf.gz + index (.tbi / .csi)*.g.vcf / .g.vcf.gz + index (.tbi / .csi) |
| Nanopore / PacBio raw | Long-read raw signal or subreads | Nanopore: .fast5 / .pod5PacBio: subreads.bam / *.bax.h5 |
| Participant-level phenotypes & consents | Individual-level clinical / phenotype data + consent terms | Consent documents (.pdf / .docx / .xlsx) |
⚠️ Note: This table is a non-exhaustive quick-reference. Companion and index files (.bai, .csi, .tbi, .crai) that enable interpretation or reconstruction of underlying controlled-access genomic data are also subject to controlled-access deposition requirements. For ambiguous cases, consult your NIH Genomic Program Administrator (GPA) before depositing. |
Updated 2 months ago
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