SRR6354578	GSE107301	GSM2870440	GPL15010-GPL21117	PMID_29358050	RNA-seq of E. coli wt cells in stationary phase 30°C (30h)	Multiscale structuring of the E. coli chromosome by nucleoid-associated and condensin proteins	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL21117: Illumina NextSeq 500 (Escherichia coli str. K-12 substr. MG1655)	data_processing	3C-seq libraries were proccessed using the 3C-seq pipeline available at (https://github.com/koszullab/). PGCGROWTHCONDITIONS
SRR6354578	GSE107301	GSM2870440	GPL15010-GPL21117	PMID_29358050	RNA-seq of E. coli wt cells in stationary phase 30°C (30h)	Multiscale structuring of the E. coli chromosome by nucleoid-associated and condensin proteins	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL21117: Illumina NextSeq 500 (Escherichia coli str. K-12 substr. MG1655)	data_processing	Removal of PCR duplicates based on the 20 first bp of the read containing a 6 nt random tag (home made script). PGCGROWTHCONDITIONS
SRR6354578	GSE107301	GSM2870440	GPL15010-GPL21117	PMID_29358050	RNA-seq of E. coli wt cells in stationary phase 30°C (30h)	Multiscale structuring of the E. coli chromosome by nucleoid-associated and condensin proteins	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL21117: Illumina NextSeq 500 (Escherichia coli str. K-12 substr. MG1655)	data_processing	Iterative alignment, Min-leght=20, step=5, bowtie2 --very-sensitive PGCGROWTHCONDITIONS
SRR6354578	GSE107301	GSM2870440	GPL15010-GPL21117	PMID_29358050	RNA-seq of E. coli wt cells in stationary phase 30°C (30h)	Multiscale structuring of the E. coli chromosome by nucleoid-associated and condensin proteins	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL21117: Illumina NextSeq 500 (Escherichia coli str. K-12 substr. MG1655)	data_processing	Filtering, Mapping quality=30, no ambiguous reads PGCGROWTHCONDITIONS
SRR6354578	GSE107301	GSM2870440	GPL15010-GPL21117	PMID_29358050	RNA-seq of E. coli wt cells in stationary phase 30°C (30h)	Multiscale structuring of the E. coli chromosome by nucleoid-associated and condensin proteins	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL21117: Illumina NextSeq 500 (Escherichia coli str. K-12 substr. MG1655)	data_processing	Assignment to restriction fragment PGCGROWTHCONDITIONS
SRR6354578	GSE107301	GSM2870440	GPL15010-GPL21117	PMID_29358050	RNA-seq of E. coli wt cells in stationary phase 30°C (30h)	Multiscale structuring of the E. coli chromosome by nucleoid-associated and condensin proteins	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL21117: Illumina NextSeq 500 (Escherichia coli str. K-12 substr. MG1655)	data_processing	Removal of un-informative events (uncuts, loops etc) as described in Cournac et al. BMC 2012. PGCGROWTHCONDITIONS
SRR6354578	GSE107301	GSM2870440	GPL15010-GPL21117	PMID_29358050	RNA-seq of E. coli wt cells in stationary phase 30°C (30h)	Multiscale structuring of the E. coli chromosome by nucleoid-associated and condensin proteins	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL21117: Illumina NextSeq 500 (Escherichia coli str. K-12 substr. MG1655)	data_processing	Binning at 5kb. PGCGROWTHCONDITIONS
SRR6354578	GSE107301	GSM2870440	GPL15010-GPL21117	PMID_29358050	RNA-seq of E. coli wt cells in stationary phase 30°C (30h)	Multiscale structuring of the E. coli chromosome by nucleoid-associated and condensin proteins	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL21117: Illumina NextSeq 500 (Escherichia coli str. K-12 substr. MG1655)	data_processing	Genome_build: E. coli MG1655 GenBank: U00096.2,total length : 4639675 bp PGCGROWTHCONDITIONS
SRR6354578	GSE107301	GSM2870440	GPL15010-GPL21117	PMID_29358050	RNA-seq of E. coli wt cells in stationary phase 30°C (30h)	Multiscale structuring of the E. coli chromosome by nucleoid-associated and condensin proteins	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL21117: Illumina NextSeq 500 (Escherichia coli str. K-12 substr. MG1655)	data_processing	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). PGCGROWTHCONDITIONS
SRR6354578	GSE107301	GSM2870440	GPL15010-GPL21117	PMID_29358050	RNA-seq of E. coli wt cells in stationary phase 30°C (30h)	Multiscale structuring of the E. coli chromosome by nucleoid-associated and condensin proteins	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL21117: Illumina NextSeq 500 (Escherichia coli str. K-12 substr. MG1655)	extract_protocol	For RNA-seq: total RNA was extracted using RNeasy Protect Bacteria according to manufacturer instructions (QIAGEN - # 74524) PGCGROWTHCONDITIONS
SRR6354578	GSE107301	GSM2870440	GPL15010-GPL21117	PMID_29358050	RNA-seq of E. coli wt cells in stationary phase 30°C (30h)	Multiscale structuring of the E. coli chromosome by nucleoid-associated and condensin proteins	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL21117: Illumina NextSeq 500 (Escherichia coli str. K-12 substr. MG1655)	extract_protocol	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). PGCGROWTHCONDITIONS
SRR6354578	GSE107301	GSM2870440	GPL15010-GPL21117	PMID_29358050	RNA-seq of E. coli wt cells in stationary phase 30°C (30h)	Multiscale structuring of the E. coli chromosome by nucleoid-associated and condensin proteins	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL21117: Illumina NextSeq 500 (Escherichia coli str. K-12 substr. MG1655)	extract_protocol	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. PGCGROWTHCONDITIONS
SRR6354578	GSE107301	GSM2870440	GPL15010-GPL21117	PMID_29358050	RNA-seq of E. coli wt cells in stationary phase 30°C (30h)	Multiscale structuring of the E. coli chromosome by nucleoid-associated and condensin proteins	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL21117: Illumina NextSeq 500 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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). PGCGROWTHCONDITIONS
SRR6354578	GSE107301	GSM2870440	GPL15010-GPL21117	PMID_29358050	RNA-seq of E. coli wt cells in stationary phase 30°C (30h)	Multiscale structuring of the E. coli chromosome by nucleoid-associated and condensin proteins	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL21117: Illumina NextSeq 500 (Escherichia coli str. K-12 substr. MG1655)	organism	Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
SRR6354578	GSE107301	GSM2870440	GPL15010-GPL21117	PMID_29358050	RNA-seq of E. coli wt cells in stationary phase 30°C (30h)	Multiscale structuring of the E. coli chromosome by nucleoid-associated and condensin proteins	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL21117: Illumina NextSeq 500 (Escherichia coli str. K-12 substr. MG1655)	source_name	E coli cells PGCGROWTHCONDITIONS
SRR6354578	GSE107301	GSM2870440	GPL15010-GPL21117	PMID_29358050	RNA-seq of E. coli wt cells in stationary phase 30°C (30h)	Multiscale structuring of the E. coli chromosome by nucleoid-associated and condensin proteins	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL21117: Illumina NextSeq 500 (Escherichia coli str. K-12 substr. MG1655)	library_strategy	RNA-Seq PGCGROWTHCONDITIONS
SRR6354578	GSE107301	GSM2870440	GPL15010-GPL21117	PMID_29358050	RNA-seq of E. coli wt cells in stationary phase 30°C (30h)	Multiscale structuring of the E. coli chromosome by nucleoid-associated and condensin proteins	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL21117: Illumina NextSeq 500 (Escherichia coli str. K-12 substr. MG1655)	characteristics	growth condition: MM + 0.12% casaminoacids +0.4% glucose at 30°C PGCGROWTHCONDITIONS
SRR6354578	GSE107301	GSM2870440	GPL15010-GPL21117	PMID_29358050	RNA-seq of E. coli wt cells in stationary phase 30°C (30h)	Multiscale structuring of the E. coli chromosome by nucleoid-associated and condensin proteins	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL21117: Illumina NextSeq 500 (Escherichia coli str. K-12 substr. MG1655)	characteristics	genotype: F- lambda- ilvG- rfb-50 rph-1 PGCGROWTHCONDITIONS
SRR6354578	GSE107301	GSM2870440	GPL15010-GPL21117	PMID_29358050	RNA-seq of E. coli wt cells in stationary phase 30°C (30h)	Multiscale structuring of the E. coli chromosome by nucleoid-associated and condensin proteins	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL21117: Illumina NextSeq 500 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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). PGCGROWTHCONDITIONS
SRR6354578	GSE107301	GSM2870440	GPL15010-GPL21117	PMID_29358050	RNA-seq of E. coli wt cells in stationary phase 30°C (30h)	Multiscale structuring of the E. coli chromosome by nucleoid-associated and condensin proteins	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL21117: Illumina NextSeq 500 (Escherichia coli str. K-12 substr. MG1655)	organism	Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
SRR6354578	GSE107301	GSM2870440	GPL15010-GPL21117	PMID_29358050	RNA-seq of E. coli wt cells in stationary phase 30°C (30h)	Multiscale structuring of the E. coli chromosome by nucleoid-associated and condensin proteins	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL21117: Illumina NextSeq 500 (Escherichia coli str. K-12 substr. MG1655)	source_name	E coli cells PGCGROWTHCONDITIONS
SRR6354578	GSE107301	GSM2870440	GPL15010-GPL21117	PMID_29358050	RNA-seq of E. coli wt cells in stationary phase 30°C (30h)	Multiscale structuring of the E. coli chromosome by nucleoid-associated and condensin proteins	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL21117: Illumina NextSeq 500 (Escherichia coli str. K-12 substr. MG1655)	contact_name	Axel,,Cournac PGCGROWTHCONDITIONS