1. Reference genome

Exact Reference genome assembly and associated index files used for alignment and downstream analyses.

2. Raw data (FASTQ)
Raw CAGE sequencing reads in FASTQ format.

*.fastq.gz

Naming convention generally follows:

<sample_id>_<run>.fastq.gz

3. CTSS (BED format) and CTSS (BAM format)

CAGE Transcription Start Sites (CTSSs) generated from aligned reads in BED format and BAM formats.

Genome coordinates and CTSS signal information.

4. Promoters data

CAGE-derived promoter annotations and expression data.

Typical contents:

promoter coordinates
promoter expression matrices
annotation tables

5. Enhancers data

CAGE-derived enhancer annotations and enhancer activity information.

Typical contents:

enhancer coordinates
bidirectional enhancer signals
enhancer activity matrices

6. CAGE-based Promoter-Enhancer interaction (BED)

Predicted promoter-enhancer interaction regions generated from CAGE co-expression and genomic proximity analyses.

These files represent putative regulatory interactions between promoters and enhancers.

7. SNPs: behavioral SNPs that are overlapped with CAGE-defined elements

8. Motif files: De novo motifs and matched motifs

motif enrichment result tables

These files are used for transcription factor binding site analyses in promoters and enhancers.