H3k4me3 from GSE86429 (hub_24769_h3k4me3)
  Position: chr1:20,762,776-20,766,776
Total Bases in view: 4,001
Statistics on: 251 items covering 2,504 bases (62.58% coverage)
Average item spans 9.98 bases. Minimum span 6 maximum span 10
Average value 2.73307 min 0 max 18 standard deviation 3.06014
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Description

This track represents the centered H3K4me3 ChIP-seq generated by de Lucas et al. (2016) and is based on the sample GSM2302418. 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 de Lucas et al. (2016) 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

de Lucas M, Pu L, Turco G, Gaudinier A, Morao AK, Harashima H, Kim D, Ron M, Sugimoto K, Roudier F, Brady SM. Transcriptional Regulation of Arabidopsis Polycomb Repressive Complex 2 Coordinates Cell-Type Proliferation and Differentiation. Plant Cell. 2016 Oct;28(10):2616-2631. Epub 2016 Sep 20. PMID: 27650334

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