2025-12-31
ENA first public
ERC000011
ENA-CHECKLIST
1. Institut Pasteur, Université Paris Cité, Plate-forme Technologique Biomics, F-75015 Paris, France 2. Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, F-75015 Paris, France
INSDC center name
public
INSDC status
ERS20600737
SRA accession
E-MTAB-14274:t1RepC2
Submitter Id
ArrayExpress
broker name
not collected
collection date
Protocols: Overnight cultures were mixed with RNAprotect (Qiagen) in the anaerobic chamber to prevent RNA degradation and bacteria were lysed using QIAGEN Proteinase K and TE buffer containing lysozyme. Bacteroides strains were grown in brain-heart infusion medium supplemented (BHIS) with cysteine 0.1%, hemin 5 μg/mL and sodium bicarbonate 0.2% (NaCOH3). Cultures were incubated statically at 37°C in a C400M Ruskinn anaerobic chamber (95% N2, 5%CO2) or in anaerobic bags (GenBag anaero, Biomerieux). E. coli strains were grown in Luria-Bertani (LB) broth (Corning) supplemented with or without ampicilin 100 μg/mL and incubated at 37°C aerobically with 180 rpm shaking. Total RNA was extracted using the Direct Zol kit (Zymo Cat. R2050) according to the manufacturer’s instructions and treated with Dnase I from the same kit. RNA concentration, quality, and integrity from 3 independent replicates were checked using the 4195 Tapestation system (Agilent). Ribosomal RNA depletion was performed using the Bacteria RiboZero Plus kit (Illumina). From rRNA-depleted RNA, directional libraries were prepared using the TruSeq Stranded Total RNA Sample preparation kit following the manufacturer’s instructions (Illumina). Libraries were checked for quality on Bioanalyzer DNA 1000 chips (Agilent). Quantification was performed with the fluorescent-based quantitation Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific)
description
NBU_DCAS9_repc
genetic modification
not collected
geographic location (country and/or sea)
not applicable
isolate
Bacteroides thetaiotaomicron
organism
Bacteroides thetaiotaomicron
organism
whole organism
organism part
Bacteroides thetaiotaomicron
scientific_name
t1RepC2
title