MNase-seq data from Li et al, 2014 (hub_24769_nucleosomes_li)
  Position: chr1:20,726,070-20,730,070
Total Bases in view: 4,001
Statistics on: 201 items covering 4,001 bases (100.00% coverage)
Average item spans 19.91 bases. Minimum span 2 maximum span 20
Average value 1.27363 min 0 max 10 standard deviation 1.84655
View table schema

Go to Nucleosomes track controls


Description

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.

Methods

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.

Credits

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 ask-epd@googlegroups.com.

References

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