[Credits]

Life Science Database Archive
FANTOM5

(reprocessed)HeliscopeCAGE sequencing, Delve mapping and CAGE TSS aggregation

Data detail

info Data name (reprocessed)HeliscopeCAGE sequencing, Delve mapping and CAGE TSS aggregation
info DOI 
info Version 
V3
V2
V1-
info Description of data contents 

Time course and snapshot data by HeliScopeCAGE
Human and mouse reads are re-mapped to new reference genome sequences (hg38/mm10).
"basic" directory contains the following:

 

00_.assay_sdrf.txt:
Experimental information for each sample (tabbed 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)
info Data file 
File name:
fantom5_rp_exp_details.zip
File URL:
https://dbarchive.biosciencedbc.jp/data/fantom5/LATEST/fantom5_rp_exp_details.zip
File size:
237 KB
File name:
(reprocessed)basic (Homo sapiens)
File URL:
https://dbarchive.biosciencedbc.jp/data/fantom5/datafiles/reprocessed/hg38_latest/basic/
File size:
1.4 TB
File name:
(reprocessed)basic (Mus musculus)
File URL:
https://dbarchive.biosciencedbc.jp/data/fantom5/datafiles/reprocessed/mm10_latest/basic/
File size:
889 GB
info Simple search URL 
info Data acquisition method 

HeliScopeCAGE (http://fantom.gsc.riken.jp/protocols/heliscope.html)
Delve (Alignment software for short read) (http://fantom.gsc.riken.jp/jp/software/)

info Data analysis method -
info Number of data entries -
Data itemDescription
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
lsid RNA Integrity number
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)