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
- 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.