Cumbie 2015, 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.



From A. thaliana (Feb 2011 TAIR10/araTha1).

Transcription Profiling data:

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

Technical Notes

Following publication guidelines each experiment was treated differently:

FASTQ files were extracted from SRA files using fastq-dump (SRA toolkit v2.5.0). After trimming, reads were mapped to TAIR10 genome using Bowtie v0.12.8. SAM files were then converted into bam using samtools v0.1.14 and to bed using bamToBed v2.12.0 (bedtools). SGA conversion was carried out using (ChIP-Seq v. 1.5.3).


Last update: 1 Oct 2018