Tokizawa 2017, Expression analysis by CAGE and Oligo-cap of several tissues.

Expression analysis by CAGE and Oligo-cap technologies of several Arabidopsis thaliana (Col-0) tissues. CAGE libraries for paired-end sequencing were prepared from roots, etiolated seedlings and light stress-treated seedlings, whereas oligo-cap libraries were prepared from leaves, roots, flower inflorescences, etiolated seedlings and light stress-treated seedlings. Tissue-specific libraries were mixed together before sequencing.

• Raw data was downloaded from: DDBJ
• Input file format: FASTQ
• Download date: 8-6-2017

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

Transcription Profiling data:

	Filename	Description	Feature	GEO-ID
1	DRX060399.sga	Various tissues|CAGE||	CAGE	-
2	DRX060400.sga	Various tissues|Oligo-cap||	Oligo-cap	-

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).

• Tokizawa M, Kusunoki K, Koyama H, Kurotani A, Sakurai T, Suzuki Y, Sakamoto T, Kurata T, Yamamoto YY
  Identification of Arabidopsis genic and non-genic promoters by paired-end sequencing of TSS tags. Plant J. 2017 May;90(3):587-605. doi: 10.1111/tpj.13511. Epub 2017 Apr 4. 28214361