Tables, figures and the draft manuscript from this repository. Code and source data are in the GitHub repository.
Generated from manuscript.tex by code/export_manuscript.py.
Open PDF on GitHubEditable version of the same draft, with references.
Download DOCX| File | Contents | Link |
|---|---|---|
astrograss_master_table.csv |
29 gravitropism candidate genes: Arabidopsis anchor and its UniProt check, Compara orthologs (Brachypodium, rice, wheat), and Su et al.'s DEG calls | Download |
candidate_spaceflight_degs.csv |
Candidate genes listed as spaceflight DEGs by Su et al. (2023): accession, organ, DESeq and edgeR values, and how the gene was matched | Download |
su2023_deg_counts.csv |
DEGs per accession, organ and direction, counted from Su et al.'s Supplemental Tables S2–S4 | Download |
astrograss_studies_catalog.csv |
Five catalogued studies (OSD-375, OSD-622, GSE97940, GSE48040, PXD000868), checked against their source records | Download |
sample_metadata.csv |
OSD-375 sample table (48 samples), parsed from the OSDR ISA metadata | Download |
cyverse_brachypodium_series.csv |
CyVerse time-lapse image series (Per1, BdTR7a) | Download |
video_catalog.csv |
Video catalogue (YouTube and CyVerse time-lapses) | Download |
astrograss_database.json |
JSON used by the AstroGrass web explorer | Download |
arabidopsis_anchor_check.csv |
UniProt check of each Arabidopsis anchor identifier | Open on GitHub |
compara_orthologs.csv |
Brachypodium, rice and wheat orthologs of each Arabidopsis anchor from Ensembl Compara (plants), with homology type and percent identity | Open on GitHub |
su2023_degs.csv |
All rows of Su et al.'s Supplemental Tables S2–S4 (6,582 DEG rows), with Ensembl gene IDs; CC BY 4.0 | Open on GitHub |
id_mapping_check.csv |
Check that Su et al.'s Phytozome gene IDs map to Ensembl identifiers | Open on GitHub |
withdrawn_bradi_id_check.csv |
Ensembl and Compara check of the withdrawn Brachypodium identifiers | Open on GitHub |
| Figure | Content | PNG | SVG |
|---|---|---|---|
| Figure 1 | OSD-375 sample design | PNG | SVG |
| Figure 2 | AstroGrass resource | PNG | SVG |
| Figure 3 | Spaceflight DEG counts from Su et al. 2023 | PNG | SVG |
| Figure 4 | Candidate genes in Su et al.'s DEG lists | PNG | SVG |
| Figure S1 | APEX-06 hardware, timeline and growth conditions | PNG | SVG |
/iplant/home/dr_richard_barker/timelapse_extract/