Guerra 2015, Genome-wide mapping of Zea mays TSSs.

Genome-wide mapping of the TSS in root and shoot from two maize lines B73 and Mo17

• Raw data was downloaded from: SRP059874
• Input file format: SRA
• Download date: 01-06-2016

From Z. mays (Oct 2013 B73 RefGen_v3/zm3).

Transcription Profiling data:

	Filename	Description	Feature	GEO-ID
1	GSM1721776.sga	B73 root|CAGE||rep1	CAGE	GSM1721776
2	GSM1721777.sga	B73 root|CAGE||rep2	CAGE	GSM1721777
3	GSM1721780.sga	Mo17 root|CAGE||rep1	CAGE	GSM1721780
4	GSM1721781.sga	Mo17 root|CAGE||rep2	CAGE	GSM1721781
5	GSM1721774.sga	B73 shoot|CAGE||rep1	CAGE	GSM1721774
6	GSM1721775.sga	B73 shoot|CAGE||rep2	CAGE	GSM1721775
7	GSM1721778.sga	Mo17 shoot|CAGE||rep1	CAGE	GSM1721778
8	GSM1721779.sga	Mo17 shoot|CAGE||rep2	CAGE	GSM1721779

FASTQ files were extracted from SRA files using fastq-dump (SRA toolkit v2.5.0) and 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. 1.5.2).

• Mejía-Guerra MK, Li W, Galeano NF, Vidal M, Gray J, Doseff AI, Grotewold E
  Core Promoter Plasticity Between Maize Tissues and Genotypes Contrasts with Predominance of Sharp Transcription Initiation Sites. Plant Cell. 2015 Dec;27(12):3309-20. doi: 10.1105/tpc.15.00630. Epub 2015 Dec 1. 26628745
• GEO series GSE70251 Genome-wide mapping of Zea maize TSSs.