2025-05-31
ENA first public
ERC000011
ENA-CHECKLIST
TBI / INSA Toulouse
INSDC center name
public
INSDC status
ERS22444146
SRA accession
E-MTAB-14542:Sample 3
Submitter Id
ArrayExpress
broker name
not collected
collection date
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).
description
not collected
geographic location (country and/or sea)
Glucose
growth condition
not applicable
isolate
Escherichia coli K-12
organism
Escherichia coli K-12
organism
3
replicate
Escherichia coli K-12
scientific_name
Sample 3
title