Genome-wide mapping of Zea mays TSSs.

Description

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

Source

Samples

From Zea mays B73 RefGene_v3 (AGPv3/zm3) Assembly.

RNA-seq 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

Technical Notes

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).

References

Last update: 19 September 2016