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.

• Raw data was downloaded from: DDBJ
• Input file format: FASTQ
• Download date: 1-6-2018

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	-

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 bed2sga.pl (ChIP-Seq v. 1.5.3).

• Ushijima T, Hanada K, Gotoh E, Yamori W, Kodama Y, Tanaka H, Kusano M, Fukushima A, Tokizawa M, Yamamoto YY, Tada Y, Suzuki Y, Matsushita T
  Light Controls Protein Localization through Phytochrome-Mediated Alternative Promoter Selection. Cell. 2017 Nov 30;171(6):1316-1325.e12. doi: 10.1016/j.cell.2017.10.018. Epub 2017 Nov 9. 29129375