This track represents the centered MNase-seq tags generated
by Li et al. (2014) and is based on the sample GSM1216733. An overview of all the tracks provided by EPD for the araTha1
assembly can be seen in table format here.
Raw data in SRA format was downloaded from GEO.
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).
The WIG file was generated with a step parameter set to 20.
Data were generated by Li et al. (2014) and processed by the
EPD team at the Swiss Institute of Bioinformatics
(Dreos et al. 2013). For inquiries, please contact us using
the online form here or
post a message on email@example.com.
Li G, Liu S, Wang J, He J, Huang H, Zhang Y, Xu L. ISWI proteins participate in the genome-wide nucleosome distribution in Arabidopsis. Plant J. 2014 May;78(4):706-14. doi: 10.1111/tpj.12499. Epub 2014 Apr 15. PMID: 24606212
Dreos R, Ambrosini G, Perier RC, Bucher P.
EPD and EPDnew, high-quality promoter resources in the
next-generation sequencing era. Nucleic Acids
Res. 2013 Jan 1;41(D1):D157-64. PMID: 23193273