Table 1.
Data files available in the data archive
| Data or analysis type | Data format | Path |
|---|---|---|
| Sample, RNA, and CAGE library information (metadata) | SDRF | /basic/*sdrf.txt |
| /basic/*CAGE/00_*assay_sdrf.txt | ||
| Ribosomal RNA hitting reads | FASTA | /basic/*CAGE/*nobarcode.rdna.fa.gz (1,385 files) |
| Mapping results (including unmapped reads) | BAM | /basic/*CAGE/*nobarcode.bam (1,385 files) |
| TSS profiles (counts of obtained 5'-end reads at 1 bp resolution) | BED | /basic/*CAGE/*ctss.bed.gz (1,385 files) |
| Sample classification based on the FANTOM Five Sample Ontology | OBO | /extra/Ontology/ff-phase1-*.obo |
| CAGE peaks (TSS clusters) | BED | /extra/CAGE_peaks/*.bed.gz |
| CAGE peak annotation (descriptions and gene association) | OSC | /extra/CAGE_peaks/*.ann.txt.gz |
| Expression of the CAGE peaks | OSC | /extra/CAGE_peaks/*.osc.txt.gz |
| Co-expression clustering | OSC | /extra/Co-expression_clusters/*_co-expression_modules.tar.gz |
| De novo motif analysis | TXT | /extra/Motifs/novel_pwms.txt |
| Sample enrichment analysis | TXT | /extra/Sample_ontology_enrichment_of_CAGE_peaks /*.txt.gz |
| Gene ontology enrichment analysis of co-expression clusters | OSC | /extra/Co-expression_clusters/*co-expression_GOstats.tar.gz |