JAXA Astronaut Cell-Free RNA Data

Until 18 October 2026 this repository held an R pipeline that derived a spaceflight oncogenic biomarker signature from 23 NASA OSDR RNA-seq studies, screened LINCS L1000 perturbation signatures for ones that reverse it, and highlighted food-derived flavonoids. A manuscript describing it was in preparation.

The manuscript and this site described the cross-study meta-analysis as a random-effects model (metafor, REML). It was not one. 33,365 genes were measured in two or more studies. For every one of them, the published meta-signature matches the Stouffer combined-z fallback in the pipeline's error handler exactly, and none matches a REML fit. The REML call failed for every gene, and the error handler substituted Stouffer's method without logging it. Stouffer's method ignores the heterogeneity between studies, species and tissues that the random-effects model was chosen to handle.

Every later result depends on that signature: the biomarker genes, the LINCS reversal scores and the flavonoid findings. Re-running the pipeline properly would mean starting again from the source data, so the analysis was withdrawn rather than corrected. The last version is kept for the record in the repository history (commit 1f16c8f).

The data are plasma cell-free RNA collected from six astronauts before, during and after ISS flight in the JAXA Cell-Free Epigenome study (OSD-530; 64 samples). The figures below come from separate iDEP analyses. The files are in the repository's data/ folder.

JAXA Astronaut Plasma cfRNA (iDEP)

iDEP analysis of astronaut plasma cell-free RNA samples taken pre-flight, in-flight (FL) and post-flight (OSD-530).

KEGG Pathway Map: Flight vs Ground Control

KEGG pathway map from an iDEP flight (FL) vs ground control (GC) comparison. TODO: the source dataset is not recorded; the astronaut cfRNA study has pre-, in- and post-flight samples but no ground control.