Tokizawa 17, Expression analysis by CAGE and Oligo-cap of several tissues.

Description

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.

Source

Samples

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

RNA-seq data:

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

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

References

Last update: 14 August 2017