1) What each platform is best for
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NCBI Submission Portal Used primarily to submit raw sequencing reads to the Sequence Read Archive (SRA) and to create/link the organizing records:
- BioProject (the overall study / project container)
- BioSample (the per-sample metadata records required for SRA)
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NCBI GEO (Gene Expression Omnibus) Best for gene expression–style datasets and processed outputs, including:
- count matrices / processed tables
- sample/ROI metadata tables
- GeoMx DSP outputs (DCC/PKC)
- supplementary analysis outputs and documentation (README, workflow description) GEO is commonly used for “processed + metadata”, while raw FASTQs (if available) go to SRA.
2) Where to submit your two dataset types
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Bulk RNA-seq (Illumina) with raw FASTQ files
- Submit to SRA via the NCBI Submission Portal.
- Ensure you have/define: BioProject + BioSamples, then upload FASTQs and metadata.
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GeoMx DSP spatial transcriptomics with only DCC/PKC + annotation Excel (+ R workflow), no FASTQs
- Submit to GEO (not SRA), because DCC/PKC are processed outputs, not raw reads.
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In GEO, upload:
- DCC files (processed counts + QC/metrics per ROI/AOI)
- PKC files (panel/probe definitions)
- annotation table (Excel is okay; CSV/TSV is even better for machine readability)
- README describing file structure + column meanings + mapping between ROI IDs and metadata
- analysis workflow (e.g., R scripts; optionally hosted on GitHub/Zenodo and linked)
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If GeoMx FASTQs are obtained later
- Submit GeoMx FASTQs to SRA, and in the GEO record state: raw reads in SRA, processed data in GEO, cross-linking accessions.
3) What to choose in the NCBI “Start a new submission” list
For your use case:
- Choose Sequence Read Archive (SRA) ✅ for FASTQ (raw reads).
- You will also use/associate BioProject and BioSample (often created during the SRA workflow).
- Do not use GenBank/TSA/Genome for these transcriptomics read submissions (those are for assembled sequences/genomes, not raw RNA-seq reads).
- GEO is not started from that list; it has its own submission entry point.
4) Accounts / login clarification
- Same login principle: In general, you use the same My NCBI account across NCBI services.
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Why GEO can feel like “another account”:
- GEO requires a GEO Submitter Profile (contact identity/profile) attached to a My NCBI account.
- In many labs, a PI or colleague already has a GEO profile under their account—so the lab might say “GEO is on another account.”
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Your options:
- Create/use your own My NCBI + GEO Submitter Profile and submit under your name.
- Or submit using the lab/PI account that already has the GEO profile (for consistent lab identity in GEO).
5) Practical “Data availability” logic for a manuscript
A journal-friendly setup is:
- Raw sequencing reads (bulk RNA-seq FASTQs; later GeoMx FASTQs if available) → SRA accession(s)
- Processed expression outputs and metadata (GeoMx DCC/PKC + annotation + processed tables) → GEO accession(s)
- Workflow/code → GitHub + DOI archive (e.g., Zenodo), linked from GEO and/or the paper.
6) ENA note (from the email context)
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If a manuscript currently lists an ENA project accession that can’t be found (e.g., looks like a placeholder), you either:
- confirm the correct existing ENA project accession, or
- create a new submission/accession (ENA or NCBI—both are widely accepted, but your processed GeoMx outputs still fit best in GEO).
7) Key takeaway (one-liner)
- FASTQ = SRA (via NCBI Submission Portal + BioProject/BioSample)
- GeoMx DCC/PKC + annotation + processed outputs = GEO
- One My NCBI login, but GEO needs a GEO Submitter Profile and uses a separate submission entry point.