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Table 1 Data files available in the data archive

From: Gateways to the FANTOM5 promoter level mammalian expression atlas

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