title: Compl_EGDe_1
organism: Listeria monocytogenes EGD-e
description: Protocols: L. monocytogenes strains were grown in 14 mL of MM under microaephilic conditions using Oxoid™ AnaeroGen™ 2.5L gas packs (Thermo Fisher) at 25 °C until the exponential phase (OD600nm = 0.4). In this condition Zea appeared slightly up-regulated compared to standard growth conditions (37 °C) (Becavin et al., 2017). A parallel culture was set-up to check the OD and arrest the bacterial growth when the strains reached the same OD. Medium was then recovered by centrifugation (2862 × g, 20 min, 4 ˚C) and filtered (0.22 M). Bacterial pellet was stored at -80 ˚C for subsequent RNA extraction. 10 mL of filtered culture medium were desalted and RNA was extracted. RNA was precipitated by adding the same volume of isopropanol and 0.3M of sodium acetate (Ambion) and 1 L of glycogen (Invitrogen). Samples were centrifuged (30 min, 10 000 × g, 4 ˚C), and RNA was washed once with 70% ethanol before being resuspended in 25 L of nuclease-free water. The quality of the RNA was checked by using Bioanalyser RNA nano kit. The amount of recovered RNA was similar in all the samples. 5 g of total secreted RNA was ribodepleted by using Ribo Zero rRNA removal kit (Illumina) following the manufacturer's instructions. Ribodepletion was controlled by Bioanalyser RNA pico kit. Directional RNA-seq libraries were prepared with 100 ng of purified RNA for each sample by using NEBNext Multiplex Small RNA Library Prep Set for Illumina according to the manufacturer's instructions.
attributes.tag: ENA-FIRST-PUBLIC
attributes.value: 2019-10-16T04:05:38Z
attributes.tag: ENA-LAST-UPDATE
attributes.value: 2019-02-11T16:07:24Z
attributes.tag: External Id
attributes.value: SAMEA5332366
attributes.tag: INSDC center name
attributes.value: Institut Pasteur - Hub Bioinformatique et Biostatistique - Centre de Bioinformatique, Biostatistique et Biologie Integrative (C3BI, USR 3756 IP CNRS) - Paris, France
attributes.tag: INSDC first public
attributes.value: 2019-10-16T04:05:38Z
attributes.tag: INSDC last update
attributes.value: 2019-02-11T16:07:24Z
attributes.tag: INSDC status
attributes.value: public
attributes.tag: Submitter Id
attributes.value: E-MTAB-7665:Compl_EGDe_1
attributes.tag: broker name
attributes.value: ArrayExpress
attributes.tag: growth condition
attributes.value: Stationnary phase
attributes.tag: sample name
attributes.value: E-MTAB-7665:Compl_EGDe_1
attributes.tag: scientific_name
attributes.value: Listeria monocytogenes EGD-e
attributes.tag: strain
attributes.value: EGD-e Compl-Zea