"3C-seq libraries were proccessed using the 3C-seq pipeline available at (https://github.com/koszullab/)."	"data_processing.1"
"Removal of PCR duplicates based on the 20 first bp of the read containing a 6 nt random tag (home made script)."	"data_processing.2"
"Iterative alignment, Min-leght=20, step=5, bowtie2 --very-sensitive"	"data_processing.3"
"Filtering, Mapping quality=30, no ambiguous reads"	"data_processing.4"
"Assignment to restriction fragment"	"data_processing.5"
"Removal of un-informative events (uncuts, loops etc) as described in Cournac et al. BMC 2012."	"data_processing.6"
"Binning at 5kb."	"data_processing.7"
"Genome_build: E. coli MG1655 GenBank: U00096.2,total length : 4639675 bp"	"data_processing.8"
"Supplementary_files_format_and_content: rna-seq: genomic position (middle of the 5kb-bin) to each count. 3C seq: contact maps (2D array of 928 5kb-bins x 928 5kb-bins)."	"data_processing.9"
"For RNA-seq: total RNA was extracted using RNeasy Protect Bacteria according to manufacturer instructions (QIAGEN - # 74524)"	"extract_protocol_ch1.1"
"For 3C-seq: ≈ 1-2 x 109 crosslinked cells (7% formaldehyde, unless otherwise stated ) are suspended in 600 μl Tris 10 mM EDTA 0.5 mM (TE) (pH 8) with 4 μl of lysozyme (35 U/μl; Tebu Bio), and incubated at RT for 20 minutes. SDS is added to the mix (final concentration 0.5%) and the cells are incubated for 10 minutes at RT. 50μl of lysed cells are then transferred in 8 tubes containing 450μL of digestion mix (1X NEB 1 buffer, 1% triton X-100, and 100U HpaII enzyme). DNA is digested for 3 hours at 37°C, split in 4 aliquots, and diluted in 8 ml ligation buffer (1X ligation buffer NEB without ATP, 1 mM ATP, 0.1 mg/ml BSA, 125 Units of T4 DNA ligase 5 U/μl). Ligation is then performed at 16°C for 4 hours, followed by incubation overnight (ON) at 65°C in presence of 250 μg/ml proteinase K and 5 mM EDTA. Precipitation of DNA is performed using an equal volume of 3 M Na-Acetate (pH 5.2) and two volumes of iso-propanol. After one hour at -80°C, DNA is pelleted, suspended in 500μl 1X TE buffer, and incubated for 30 minutes at 37°C in presence of RNAse A (0.03 mg/ml). DNA is then transferred into 2 ml centrifuge tubes, extracted twice with 500 μl phenol-chloroform pH 8.0, precipitated, washed with 1 ml cold ethanol 70% and diluted in 30 μl 1X TE buffer. All tubes are pooled and the resulting 3C library is quantified on gel using Quantity One software (BioRad)."	"extract_protocol_ch1.2"
"3C-seq: 5 µg of a 3C library was suspended in water (final volume 130 µL) and sheared using a Covaris S220 instrument (Duty cycle 5, Intensity 5, cycles/burst 200, time 60 sec for 4 cycles). The DNA was purified and processed according to manufacturer instructions (Paired-End DNA sample Prep Kit – Illumina – PE-930-1001), except that DNA was ligated to custom-made adapters (see Marbouty M. et al, 2015, Mol Cell) for 4 hours at room temperature. Tubes were then incubated at 65°C for 20 minutes. DNA fragments ranging in size from 400 to 900 pb were purified using a PippinPrep apparatus (SAGE Science). For each library, four test PCR reactions were performed to determine the optimal number of PCR cycles (1 or 2 µL of the collected DNA, Illumina primers PE1.0 and PE2.0 using Taq Phusion [Finnzymes]). A large-scale PCR (8 reactions) was then set-up with the number of PCR cycles determined previously. The PCR product was finally purified on Qiagen MinElute columns and subject to paired-end sequenced on an Illumina sequencer."	"extract_protocol_ch1.3"
"E. coli cells were grown at 22°C, 30°C and 37°C in either Lennox Broth (LB) or liquid minimal medium A supplemented with 0.12% casamino acids and 0.4% glucose. The cultures were grown to OD600 = 0.2 (early exponential) or 2 (stationary phase)."	"growth_protocol_ch1.1"
"Escherichia coli str. K-12 substr. MG1655"	"organism_ch1.1"
"E coli cells"	"source_name_ch1.1"
"RNA-seq of E. coli wt cells in stationary phase 30°C (30h)"	"title.1"
"RNA-Seq"	"library_strategy.1"
"growth condition: MM + 0.12% casaminoacids +0.4% glucose at 30°C"	"characteristics_ch1.1"
"genotype: F- lambda- ilvG- rfb-50 rph-1"	"characteristics_ch1.2"
"E. coli cells were grown at 22°C, 30°C and 37°C in either Lennox Broth (LB) or liquid minimal medium A supplemented with 0.12% casamino acids and 0.4% glucose. The cultures were grown to OD600 = 0.2 (early exponential) or 2 (stationary phase)."	"growth_protocol_ch1.1"
"Escherichia coli str. K-12 substr. MG1655"	"organism_ch1.1"
"E coli cells"	"source_name_ch1.1"