2024-10-19
ENA first public
ERC000011
ENA-CHECKLIST
SAMEA114531511
External Id
Institute for Integrative Biology of the Cell (I2BC) University Paris-Saclay
INSDC center name
2023-10-25T11:35:33Z
INSDC last update
public
INSDC status
ERS16512845
SRA accession
E-MTAB-13482:MA14692_1_AHTc
Submitter Id
ArrayExpress
broker name
not collected
collection date
Protocols: Overnight bacterial cultures in LB broth were diluted 1:200 in LB or in LB broth supplemented with 0.4 µg/ml Anhydrotetracycline (AHTc) and grown with shaking at 37°C to an OD600 = 0.7 to 0.8. Cultures (4 ml) were rapidly centrifuged and resuspended in 0.6 ml ice-cold REB buffer (20 mM Sodium Acetate pH 5.0, 10% sucrose). RNA was purified by sequential extraction with one volume (0.6 ml) of hot acid phenol, phenol-chloroform 1:1 mixture and chloroform. Following overnight ethanol precipitation at -20°C and centrifugation, the RNA pellet was resuspended in 20 µl of H2O. Three samples were prepared from independent biological replicates for each strain and condition. RNA yields, measured by Nanodrop reading, typically ranged between 2 and 3 µg/µl. RNA (1 µg) was combined with 1 µl of a mixture of primer AI69 (hilD-specific) and AM99 (leuO-specific) 5 µM each and 1 µl of 10 mM dNTPs in a 6 µl final volume. After a 5 min treatment at 70°C (in a Thermocycler), samples were quickly cooled on ice. Each sample were then mixed with 2.5 µl of Template Switching Buffer (4x), 0.5 µl of 75 µl of Template Switching Oligonucleotide (TSO; AI39) and 1 µl of Template Switching RT Enzyme Mix in a final volume of 10 µl. Reverse transcription was carried out for 90 min at 42°C, followed by a 5 min incubation at 85°C. The cDNAs were amplified in parallel with a common forward primer (AK47, annealing to the TSO) and a reverse primer specific for the region being analyzed and carrying a treatment-specific index sequence. PCR reactions were set up according to New England Biolabs PCR protocol for Q5 Hot Start High-Fidelity DNA polymerase in a final volume of 50 µl (using 1 µl of the above cDNA preparation per reaction). The PCR program was as follows: activation: 98°C for 30 sec; amplification (30 cycles, hilD or 35 cycles, leuO): 98°C for 10 sec; 65°C for 15 sec; 72°C for 30 sec; final stage: 72°C for 5 min.
description
tetRA-Term upstream hilD
genotype
not collected
geographic location (country and/or sea)
Lysogency Broth (LB) plus Anhydrotetracycline (0.4 µg/ml)
growth condition
not applicable
isolate
Salmonella enterica subsp. enterica
organism
Salmonella enterica subsp. enterica
organism
whole organism
organism part
Salmonella enterica subsp. enterica
scientific_name
MA14692
strain
MA14692_1_AHTc
title