Cumbie 15, Nano-CAGE data of Arabidopsis roots


A new CAGE technique is been developed (NanoCAGE-XL) that promises the identification of high confidence transcription start sites. This is a proof-of-concept dataset.


Data available at: GEO

Input file formats : SRA


From Arabidopsis at10 (araTha1) Assembly

Filename Description Feature GEO-ID
1 SRX815832.sga 9-day old roots|exp1 CAGE -
2 SRX1097403.sga 9-day old roots|exp2 CAGE -
3 SRX1097494.sga 9-day old roots|exp3 CAGE -

Technical Notes

Following publication guidelines each experiment was treated differently:

After trimming, reads were mapped to TAIR10 genome using bowtie2. The resulting SAM files were converted to BED using SAMtools and BEDtools. Final conversion to SGA files was done using ChIP-Seq.


  1. Cumbie JS, Ivanchenko MG, Megraw M

    NanoCAGE-XL and CapFilter: an approach to genome wide identification of high confidence transcription start sites. BMC Genomics. 2015 Aug 13;16(1):597. PMID: 26268438