CoSE Space Omics NASA OSDR Plant miRNA scan: not interpretable yet Zenodo DOI pending

smallRNAseq-DREAM

A cross-species small RNA-seq (miRNA) analysis framework, with an inventory of NASA Open Science Data Repository (OSDR) plant RNA-seq studies.

GitHub Repository Status Dataset Inventory Figures Reproducibility & Data
12OSDR plant RNA-seq studies indexed
0plant small RNA-seq studies in OSDR (2026-07 survey)
176OSDR studies matched by small-RNA search terms
4analysis engines consolidated (benchmark pending)

01Status of the Plant miRNA Scan

The plant miRNA outputs in this repository are not interpretable yet. An evidence check on 2026-10-28 found three problems:

  • OSD-437 is standard poly(A) RNA-seq, not small RNA-seq. Its OSDR record lists one RNA-Seq assay (19 samples, library selection "polyA enrichment", NEB Next Ultra II RNA Library Prep Kit). OSDR holds no plant small RNA-seq.
  • The locus map mislabels most IDs. Of the 29 IDs the hand-typed map labels as MIR genes, 3 are the named MIR gene. 16 are protein-coding (for example AT1G53160 is SPL4, labelled "MIR156b"), 2 are lncRNA, 1 is snoRNA and 7 are a different MIR gene (Ensembl Plants lookup).
  • The fold changes are not flight vs ground. The scan uses the first contrast in each GeneLab table. For OSD-437 that is 1g centrifuge vs microgravity, both in flight. For OSD-120, OSD-218, OSD-565 and OSD-782 it compares ground or treatment groups. For OSD-217 it is ground vs flight, the reverse orientation.

TODO: rebuild the locus map from Ensembl Plants miRNA genes, select each study's flight-vs-ground contrast by name, then regenerate the tables and figures. Until then, no miRNA result from this scan should be cited.

02The Recommended Pipeline Route

From hands-on testing of four small RNA-seq analysis engines (nf-core/smrnaseq, sRNAtoolbox, miRDeep2, miRDeep-P2), the author recommends this route for cross-species analysis. The quantitative four-engine benchmark has not been run yet.

SRA → mirnaQC → sRNAbench → sRNAde → mirNOVO

nf-core/smrnaseq runs under Nextflow's container profiles. The original SLURM/OSDR cluster script was lost before consolidation, and the sRNAtoolbox Singularity definition is still to be added.

03NASA OSDR Plant Dataset Inventory

Twelve plant RNA-seq studies in NASA OSDR: 9 spaceflight, 1 suborbital (high-altitude) and 2 ground studies, across Arabidopsis thaliana, Brachypodium distachyon, Solanum lycopersicum and Brassica rapa. Values are read from each study's OSDR record (2026-10-28). "Samples" counts the samples in the study's RNA-Seq assay; a blank cell means the record has no value.

StudySpeciesOSDR project typeMissionPlatformSamplesLibrary selection
OSD-437Arabidopsis thalianaSpaceflight StudySpaceX-9European Modular Cultivation System (EMCS), Experimental Reference Module (ERM2)19polyA enrichment
OSD-120Arabidopsis thalianaSpaceflight StudySpaceX-336ribo-depletion
OSD-218Arabidopsis thalianaSpaceflight StudySpaceX-5Vegetable Production System (VPS/Veggie)32polyA enrichment
OSD-217Arabidopsis thalianaSpaceflight StudySpaceX-5Vegetable Production System (VPS/Veggie)12cDNA
OSD-375Brachypodium distachyonSpaceflight StudySpaceX-14Vegetable Production System (VEGGIE), APEX Growth Unit48Ribo-depletion (32), cDNA (16)
OSD-480Arabidopsis thalianaSpaceflight StudySpaceX-13European Modular Cultivation System (EMCS)400
OSD-522Arabidopsis thalianaSpaceflight StudySpaceX-13, SpaceX-14BRIC-LED12polyA enrichment
OSD-565Arabidopsis thalianaGround StudyKSC Fixation Tubes (KFTs)45cDNA
OSD-624Arabidopsis thalianaHigh Altitude StudyUnity 22Kennedy Space Center Fixation Tubes (KFTs)36polyA enrichment
OSD-767Solanum lycopersicumSpaceflight StudySpaceX-26Vegetable Production System (Veggie)36polyA enrichment
OSD-782Arabidopsis thalianaGround Study36polyA enrichment
OSD-59Brassica rapaSpaceflight StudyExpedition 22Lada2mRNA enrichment
Figure 1: indexed OSDR plant studies by species and by RNA-seq library selection
Figure 1. The 12 indexed OSDR plant studies. (A) Studies by species. (B) RNA-seq library selection as recorded in each study's OSDR ISA record; one study (OSD-480) records none.

04Exploratory miRNA Scan (Not Interpretable Yet)

These figures plot the scan's current tables. They are kept so the TODO above can be checked against them, not as results.

Figure 2: log2 fold change of rows labelled as MIR genes by the typed locus map
Figure 2. Rows labelled as MIR genes by the typed locus map (most are not miRNA genes). (A) log2FC against −log10 P for the first contrast in each GeneLab table, which is not flight vs ground. (B) log2FC by map label and study; 0.00 marks a missing row.
Figure 3: sign of log2 fold change for curated miRNA-target pairs
Figure 3. 115 study-level pairings of 24 hand-curated literature miRNA–target pairs. The x-axis is the mean log2FC of the matching map-labelled rows (mostly not miRNA genes); the y-axis is the target gene's log2FC. 45 of the 115 have opposite signs. No correlation is claimed.

05Illustrative Fisher Test

For each pathway, a Fisher exact test compares the pairs whose target has P ≤ 0.05 against a typed background of 25,000 genes and 3,500 "DE" genes, assumed rather than measured, and each target is counted once per study. The p-values are therefore illustrative, not an enrichment result. TODO: use each study's measured gene universe and DE set.

Figure 4: illustrative Fisher test under a typed background
Figure 4. Illustrative Fisher test under the typed background; not an enrichment result.

06Schematics and Network View

Figure 5: schematic of literature miRNA to target to process relationships
Figure 5. Schematic, no data: literature miRNA → target → process relationships.
Figure 6: graph of curated miRNA-target pairs and pathway hubs
Figure 6. Graph of the curated miRNA–target pairs and pathway hubs. Node values are mean log2FC of the first deposited contrast; miRNA nodes use mislabelled loci.
Figure 7: schematic auxin and ROS pathway map
Figure 7. Schematic pathway map. Bracketed values are table means of the first deposited contrast (not flight vs ground; miRNA rows mislabelled). Phenotype and stress boxes carry no data.

07Reproducibility & Data

The smallRNAseq-DREAM code is open source under the MIT License. All input data are public NASA OSDR datasets.

Pipeline Driver

Regenerates the inventory, the scan tables and Figures 1–7 from OSDR downloads:

python run_pipeline.py

Zenodo Deposit & Citation

Citation metadata are in .zenodo.json and CITATION.cff. A Zenodo deposit of the benchmark bundle is prepared but not yet made.

Zenodo DOI: pending