biostudies-arrayexpressAnne StringerEscherichia coli str. K-12 substr. MG1655https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16502We used ATAC-seq to identify the genome-wide binding of CRP in E. coli MG1655biostudies-arrayexpressSequencing - Sequencing was performed on an Illumina Next-Seq Instrument (Wadsworth Center Applied Genomics Technologies Core).Library Construction - PCR amplify DNA in a 50ul reaction using the Nextera® DNA Library Prep Kit (Illumina, San Diego, CA), following the manufacturer’s instructions (2016 version). The kit included custom Nextera PCR primers. Cycling parameters are as follows: 1X 72C for 5 minutes, 98C for 30 seconds 6X 98C for 10 seconds, 63C for 30 seconds, 72C for 1 minute.Sample Collection - reaction conditions: 50ng DNA, 1X binding buffer (160mM HEPES (pH 8.0, 20 mM MgCl2, 400 mM potassium glutamate), 0.2 mM cAMP, and varying concentrations of CRP protein in CRP stock buffer(10mM sodium phosphate (pH 6.8), 0.1 mM EDTA, 0.2M NaCl, 50% (w/v) glycerol). Incubate 37C 10 minutes. Then 5ul TDE1 Nextera transposase is added and the reaction is incubated at 37C for 30 more minutes.Nucleic Acid Extraction - The DNA from the reaction is purified with a Qiagen MinELute kit. DNA is eluted in 10ul elution buffer.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Custom python code was used to generate gff files, allowing read density to be visualized at every position of the genome.Data Transformation - Rockhopper is 2.03 was used to align fastq reads to the E. coli K12 MG1655 genome to generate .sam files.Sequence Alignment - Rockhopper is 2.03 was used to align fastq reads to the E. coli K12 MG1655 genome to generate .sam files.MetabolomicsUnknownTranscriptomicsGenomicsProteomicsNextSeq 1000RNA-seq of coding RNAEscherichia coli str. K-12 substr. MG1655Anne StringerfalseE. coli CRP Footprint-seqWe used ATAC-seq to identify the genome-wide binding of CRP in E. coli MG16552026-01-13T00:00:00Z2026-05-26T19:01:39.84Z2026-01-02T15:19:26.388ZE-MTAB-16502EFO_0002944EFO_0004170EFO_0004917EFO_0005518EFO_0003816EFO_0003738EFO_0004184