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 root|B73|rep1 CAGE -
2 GSM1721777.sga root|B73|rep2 CAGE -
3 GSM1721780.sga root|Mo17|rep1 CAGE -
4 GSM1721781.sga root|Mo17|rep2 CAGE -
5 GSM1721774.sga shoot|B73|rep1 CAGE -
6 GSM1721775.sga shoot|B73|rep2 CAGE -
7 GSM1721778.sga shoot|Mo17|rep1 CAGE -
8 GSM1721779.sga shoot|Mo17|rep2 CAGE -

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: 14 Jun 2016