ERC000011
ENA-CHECKLIST
2024-02-23T13:48:53Z
ENA-FIRST-PUBLIC
2024-02-23T13:48:53Z
ENA-LAST-UPDATE
SAMEA114857184
External Id
Department of Microbial Genetics and Gene Expression, Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
INSDC center name
2024-02-23T13:48:53Z
INSDC first public
2024-02-23T13:48:53Z
INSDC last update
public
INSDC status
ERS17282143
SRA accession
E-MTAB-13608:Cg-ST10-SigA
Submitter Id
ArrayExpress
broker name
not collected
collection date
Protocols: 40 ml cells from exponential phase or 35 ml cells from stationary phase were pelleted and washed in lysis buffer (20 mM Tris–HCl pH 7.9, 150 mM KCl, 1 mM MgCl2, 1 mM dithiothreitol (DTT) and frozen in -70°C. Corynebacterium glutamicum ATCC 13032 (wt, LK1100) were grown at 30°C in 2x YT medium and harvested in exponential (OD600 ∼1) or early stationary phase (OD600 >10, ∼26 hrs of cultivation). Cells resuspended in lysis buffer (20 mM Tris–HCl pH 7.9, 150 mM KCl, 1 mM MgCl2, 1 mM dithiothreitol (DTT), 0.5 mM phenylmethylsulfonyl fluoride (PMSF), supplemented with Calbiochem Protease Inhibitor Cocktail Set III protease inhibitors), sonicated 20 × 10 s with 1 minute pauses on ice and centrifuged. 3 mg (protein) of lysates were incubated for 16-18 hours at 4°C with 20 μl of Protein G plus agarose beads (Santa Cruz) coated with 5 μg mouse monoclonal anti-beta subunit of RNAP antibody [clone 8RB13] (Biolegend), 2.5 μg of anti-Sigma70 antibody [clone 2G10] (Biolegend), or 5 μg of mouse nonspecific IgG (Sigma-Aldrich) used as a negative control, respectively. The captured complexes were washed four times using 20 mM Tris–HCl pH 7.9, 150 mM KCl, 1 mM MgCl2, finally resuspended in 200 μl 1% SDS, 150 mM KCl, 20 mM Tris–HCl pH 7.9, 1 mM MgCl2 and incubated on a rotating platform with 200 μl acidic phenol (pH∼3):chloroform (1:1) for 15 minutes. Eluted RNA was precipitated with ethanol, dissolved in water and DNase treated (TURBO DNA-free Kit, Ambion). Inputs are total RNA samples isolated from the bacterial lysates. 10% of lysate that was used for one immunoprecipitation was diluted in 1% SDS, 20 mM Tris–HCl pH 7.9, 150 mM KCl, 1 mM MgCl2 to final volume 200 μl and RNA was isolated with the same protocol as the immunoprecipitated RNA. 14 ul of RNA sample was used for library construction according to the NEXTFLEX® Rapid Directional RNA-Seq Kit. For input samples, 100 ng of RNA was used for library construction. DNA concentrations of IgG control libraries were not measurable, therefore these libraries were not sequenced.
description
not collected
geographic location (country and/or sea)
stationary phase
growth condition
not applicable
isolate
Corynebacterium glutamicum ATCC 13032
organism
Corynebacterium glutamicum ATCC 13032
organism
whole organism
organism part
3
replicate
Corynebacterium glutamicum ATCC 13032
scientific_name
Cg-ST10-SigA
title