title: Sample 1
organism: Escherichia coli K-12
description: Protocols: 4 x 10^9 cells were centrifuged at 13,000 rpm for 2 minutes and pellets were flash frozen in liquid nitrogen. Escherichia coli strain BW25113 was grown on minimal M9 medium with either glucose (15 mM), xylose (18 mM), or a mix of glucose (6 mM) and xylose (11 mM). M9 medium contains 33.7 mM Na2HPO4, 22 mM KH2PO4, 8.55 mM NaCl, 9.35 mM NH4Cl, 1 mM MgSO4, 0.3 mM CaCl2, 13.4 mM EDTA, 3;1 mM FeCl3-6H2O, 0.62 mM ZnCl2, 76 μM CuCl2-2H2O, 42 μM CoCl2-2H2O, 162 μM H3BO3, 8.1 μM MnCl2-4H2O, 1 μg.L-1 thiamine and carbon sources as described above. M9 medium was supplemented with 20 mg.L-1 chloramphenicol to maintain the plasmid pBR322 PihfB-mTagBFP PxylA-mRFP1.   Growths were performed in 1L bioreactors (pH 7, 37°C, pO2>20%). Inoculations were done at 0.03 OD 600 nm and sampling was performed between OD 0.5 and 1. Three independent repetitions led to three biological replicates per conditions.  Cells were thawed on ice and suspended in Tris-EDTA (TE) buffer, then mechanically lysed using Fastprep (MP Biomedical) with glass beads. RNA extraction was carried out by adding Trizol and phenol. Potential DNA contamination was eliminated using the TURBO DNA-freeTM kit (Ambion). ERCC (ERCC RNA Spikes-In Control Mix 1, AMBION) was added before ribodepletion with 1 μL of ERCC diluted 1/10 for 5000 ng of total RNA. Ribodepletion was performed with the Pan-Karyote SiTools ribo POOL kit (siTOOLs Biotech). 10 ng ribodepleted RNA was used to construct a sequencing library using the Ion Total RNA-Seq Kit v2 Kit and the Ion Xpress™ RNA-Seq Barcode 1-16 Kit (Thermo Fisher Scientific, Waltham, MA, USA).
attributes.tag: ENA first public
attributes.value: 2025-05-31
attributes.tag: INSDC center name
attributes.value: TBI / INSA Toulouse
attributes.tag: INSDC status
attributes.value: public
attributes.tag: Submitter Id
attributes.value: E-MTAB-14542:Sample 1
attributes.tag: broker name
attributes.value: ArrayExpress
attributes.tag: collection date
attributes.value: not collected
attributes.tag: geographic location (country and/or sea)
attributes.value: not collected
attributes.tag: growth condition
attributes.value: Glucose
attributes.tag: isolate
attributes.value: not applicable
attributes.tag: replicate
attributes.value: 1
attributes.tag: sample name
attributes.value: E-MTAB-14542:Sample 1
attributes.tag: scientific_name
attributes.value: Escherichia coli K-12