Time course and snapshot data by HeliScopeCAGE
"basic" directory contains the following:
Subdirectories with "CAGEScan" in end (only human)
Subdirectories expect above
HeliScopeCAGE (http://fantom.gsc.riken.jp/protocols/heliscope.html)
CAGEscan(http://fantom.gsc.riken.jp/protocols/nanocage.html)
Delve (Alignment software for short read) (http://fantom.gsc.riken.jp/jp/software/)
| Data item | Description |
|---|---|
| Extract name | Internal ID |
| FF ontology | Ontology ID in FANTOM |
| Description | Description |
| Catalog ID | RNA catalog ID |
| Category | Category |
| Species | Species |
| Sex | Sex |
| Age | Age |
| Developmental stage | Developmental stage |
| Tissue | Tissue |
| Cell lot | Cell lot |
| Cell type | Cell type |
| Catalogue ID | Cell catalogue ID |
| Collaboration | Collaboration |
| Provider | Cell provider |
| Extraction protocol | RNA extraction protocol |
| Material type | RNA Material type |
| RNA tube | RNA tube ID (the same as Extact name) |
| Sample name | Sample name |
| RNA extraction | RNA extraction |
| RNA ID | Internal RNA ID |
| Comment on RNA | Comment on RNA |
| ratio_260/230 | Ratio (260nm/230nm) of the sample |
| ratio_260/280 | Ratio (260nm/280nm) of the sample |
| Concentration | RNA concentration |
| RNA Integrity number | RNA Integrity number |
| lsid | Sample group ID |
| Library protocol | Library protocol |
| Library ID | Library ID |
| Sequence protocol | Sequence protocol |
| Machine name | Machine name |
| Run name | Run name |
| Flowcell channel | Flowcell channel |
| Alignment protocol | Alignment protocol |
| BAM file | Read mapping results (BAM format) |
| BAI file | Index of BAM file |
| CAGE TSS file | TSS identified by CAGE analysis (BED format) |
| Ribosomal DNA sequence file | rDNA sequence file (FASTA format) |
| Barcode | Barcode sequence for RNA sample identification |