Ushijima 2017, Transcription profiling of WT and phy mutant plants grown in red light.


WT Col-0 and phyAphyB mutant plants were grown under different red light conditions (1h, 3h, continuous) and transcript profiled using CAGE.



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

Transcription Profiling data:

Filename Description Feature GEO-ID
1 DRS056268.sga WT|Red|1h CAGE -
2 DRS056269.sga WT|Red|3h CAGE -
3 DRS056270.sga WT|continuous Red CAGE -
4 DRS056271.sga phyAphyB|Red|1h CAGE -
5 DRS056272.sga phyAphyB|Red|3h CAGE -
6 DRS056273.sga phyAphyB|continuous Red CAGE -

Technical Notes

FASTQ files were mapped to the 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: 8 Oct 2018