Bacterial regulons in Escherichia coli with ChIP-seq and RNA-seq

Publication

Myers KS, Park DM, Beauchene NA, Kiley PJ. Defining bacterial regulons using ChIP-seq. Methods. 2015 Sep 15;86:80-8. doi: 10.1016/j.ymeth.2015.05.022. Epub 2015 May 29. Review. PubMed PMID: 26032817; PubMed Central PMCID: PMC4577457.

• PubMed PMID: 26032817
• PubMed Central PMCID: PMC4577457

Data availability

Raw reads

GEO series GSE41195

**Subsets:**

- [GSE41186](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE41186): Chip-chip from Escherichia coli MG1655 K-12, WT and ∆fnr strains

- [GSE41187](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE41187)	Genome-wide analysis of FNR and σ70 in E. coli under aerobic and anaerobic growth conditions.

- [GSE41189](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE41189)	Expression analysis of Escherichia coli MG1655 K-12 WT and ∆fnr mutant

Reference genome

We download the reference genome from EnsemblGenomes Bacteria, release 37, strain and assembly identifier Escherichia_coli_str_k_12_substr_mg1655.ASM584v2.

• Genome sequence (fasta format)
• Genome annotations (GFF3 format)
• Genome annotations (GTF format)

Preprocessed dataset

We prepared a few small datasets that can be used for some courses for quick tests.

ChIP-seq

• Genome coverage files (wig fixed step format)

  • FNR_200bp.wig
  • input_200bp.wig

• Peaks returned by MACS2 and Homer peak-callers, resp. (bed format)

  • FNR1_vs_input1_cutadapt_bowtie2_homer.bed
  • FNR1_vs_input1_cutadapt_bowtie2_macs2.bed

RNA-seq

• Counts per gene (tab-separated value format)

  • cutadapt_bwa_featureCounts_all.tsv