Time course and snapshot data by HeliScopeCAGE
"basic" directory contains the following:

Subdirectories with "CAGEScan" in end (only human)

00_.assay_sdrf.txt:

Experimental information for each sample (tab-delimited text)

*.bam:

Binary read mapping results (BAM format)

*.bam.bai:

Indexes of BAM files

*.3prime.fq.gz:

3' sequences in CAGEscan tags (FASTQ format)

*.5prime.fq.gz:

5' sequences in CAGEscan tags (FASTQ format)

*.clusters.bed.gz

Clustering results with CAGEscan (standard BED12 format). 4th column shows the CAGE tag name that represents the cluster and 5th column shows the number of pairs that constitute the cluster.

*.pairs.bed.gz

Read pairs mapped with CAGEscan (standard BED12 format). 4th column shows the pair's name and 5th column shows the total mapping quality value of reads.

Subdirectories expect above

00_.assay_sdrf.txt:

Experimental information for each sample (tab-delimited text)

*.bam:

Binary read mapping results (BAM format)

*.bam.bai:

Indexes of BAM files

*.ctss.bed.gz:

TSS (CTSS) identified by CAGE tag analysis (BED format)

*.rdna.fa.gz:

rDNA sequences (FASTA format)