"genotype/variation: wild type"	"characteristics_ch1.1"
"strain: K12"	"characteristics_ch1.2"
"Library strategy: REC-Seq"	"data_processing.1"
"genome build: NC_000913.3"	"data_processing.2"
"To remove contaminating sequences, the reads were split according to the HinfI consensus motif (5’-  G^ANTC-3’) considered as a barcode sequence using fastx_toolkit  (http://hannonlab.cshl.edu/fastx_toolkit/) (fastx_barcode_splitter.pl --bcfile barcodelist.txt --bol --  exact). Most of the reads (more than 90%) were rejected, and the reads kept were remapped to the  reference genomes with bwa mem and samtools to generate a sorted bam file.  The bam file was further filtered to remove low mapping quality reads (keeping AS >= 45) and split  by orientation (alignmentFlag 0 or 16) with bamtools. The reads were counted at 5' positions  using Bedtools (bedtools genomecov -d -5). Both orientation count files were combined into a  bed file at each identified 5’-GANTC-3’ motif (where reverse counts >=1 at position N+1 and forward  counts >=1 at position N-1) using a home-made PERL script. The HinfI positions in the bed file were  associated with the closest gene using Bedtools closest and the gff3 file of the reference genomes  . The final bed file was converted to an MS Excel sheet (S1 and S2 Tables) with a homemade  script. For the MboI-based REC-Seq, the strategy was identical except that a different adaptor was  used for ligation after cleavage and the MboI consensus motif (5’-^GATC-3’) was used as barcode for  filtering of V. cholerae O1 biovar El Tor and E. coli K12 Ec100D gDNA mapped onto the  MG1655 genome."	"data_processing.3"
"Supplementary_files_format_and_content: tab delimited text files, with feature annotation, REC_seq score, gene name and description"	"data_processing.4"
"For REC-Seq (restriction enzyme cleavage–sequencing) 1 ug of genomic DNA from C.  crescentus NA1000 and S. meliloti Rm2011 was cleaved with HinfI, a blocked (5’biotinylated)  specific adaptor was ligated to the ends and the ligated fragments were then sheared to an average size  of 150-400 bp (Fasteris SA, Geneva, CH). Illumina adaptors were then ligated to the sheared ends  followed by deep-sequencing using a Hi-Seq Illumina sequencer, and the (50 bp single end) reads  were quality controlled with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)."	"extract_protocol_ch1.1"
"DNA libraries were prepared for sequencing using standard Illumina protocols by FASTERIS SA, Switzerland"	"extract_protocol_ch1.2"
"Caulobacter crescentus and derivatives were grown at 30°C in PYE (Peptone yeast extract) or LB"	"growth_protocol_ch1.1"
"Escherichia coli str. K-12 substr. MG1655"	"organism_ch1.1"
"Escherichia coli MG1655"	"source_name_ch1.1"
"GHA507"	"title.1"
"OTHER"	"library_strategy.1"
"genotype/variation: wild type"	"characteristics_ch1.1"
"strain: K12"	"characteristics_ch1.2"
"Caulobacter crescentus and derivatives were grown at 30°C in PYE (Peptone yeast extract) or LB"	"growth_protocol_ch1.1"
"Escherichia coli str. K-12 substr. MG1655"	"organism_ch1.1"
"Escherichia coli MG1655"	"source_name_ch1.1"