Data Files
Atlas data matrices (data/)
Large files not tracked in git. Obtain from GEO accession GSE308970.
| File |
Dimensions |
Description |
GSE308970_TPM_Atlas_allbatches_merged_v3.csv |
~25K genes × 677 samples |
TPM-normalized expression matrix |
GSE308970_rawcount_Atlas_allbatches_merged_v3.csv |
~25K genes × 677 samples |
Raw count matrix |
ExperimentDesign_allbatches_combined_v7.csv |
677 rows |
Sample metadata: tissue, age_days, sex, batch |
| Column |
Values |
Notes |
tissue |
Brain, Eye, SpinalCord, Heart, Lung, Liver, Gut, Fat, Kidney, Spleen, Muscle, Skin, Bone, Testis, Ovary |
15 tissues |
age_days |
47–163 |
Killifish lifespan: ~3–6 months |
sex |
F, M |
Some tissues are single-sex (Testis=M, Ovary=F) |
batch |
integer |
Sequencing batch number (used by ComBat-seq) |
Gene mapping files
Files tracked in git. Used to map query Ensembl IDs → Atlas gene names.
| File |
Description |
gene_id_map.csv |
Full unified mapping table (GTF + NCBI + Atlas) |
query_to_atlas_gene_mapping.csv |
Ensembl ID → Atlas gene name (direct input for GeneMapper) |
ncbi_gene2ensembl_nfurzeri.csv |
NCBI gene2ensembl table for N. furzeri |
GCF_043380555.1_NfurGRZ-RIMD1_genomic.gtf |
GTF annotation for NfurGRZ-RIMD1 assembly |
build_gene_map.py |
Script that produced gene_id_map.csv |
See Gene ID Mapping for the full mapping pipeline.
Query data (query_data/)
| File |
Description |
toy.csv |
Minimal toy count matrix for testing run_query_clocks.py |