|
| Status |
Public on Jan 26, 2023 |
| Title |
E. coli cell, envZ_point_mutant, rep3 |
| Sample type |
SRA |
| |
|
| Source name |
envZ_Val241Gly
|
| Organism |
Escherichia coli |
| Characteristics |
cell line: envZ_Val241Gly
cell type: point mutant
genotype: BW25113
|
| Treatment protocol |
In the case of CC1_120, CC2_120 and CC3_120 lines, log phase cells of the ancestor were treated with a lethal concentration of ciprofloxacin (50 ng/ml) for 120 minutes.
In the case of CC1_0, CC2_0 and CC3_0 lines, log phase cells were treated with ciprofloxacin (50 ng/ml), and harvested immediately (0 minutes).
|
| Growth protocol |
Strains were grown in Minimal salts (MS) medium supplemented with 0.1mM MgSO4, 0.54 μg/mL FeCl3, 1 μg/mL Tiamin, 0.2% Cas amino-acids and 0.2% glucose.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cultures were started from single colonies and grown overnight in Erlenmeyer flasks (25 ml minimal medium). Approximately 109 cells (A600 nm ≈ 1) were taken as samples for RNA isolation. RNA was isolated in late exponential phase (OD around 0.8-1). QIAGEN RNA Protect bacteria reagent was used for freezing of samples (Cat. Num.: 76506). Macherey-Nagel NucleoSpin RNA Plant kit was used for RNA isolation (Cat. Num.: 740949.50). And additional DNase treatment was carried out with Ambion DNase I (Cat. Num.: AM2222). All steps were carried out according to the Manufacturer's instructions.
Ribo-Zero rRNA Removal Kit (Gram-Negative Bacteria, Cat.Num.: MRZGN126) was used for RNA depletion. SOLiD Total RNA-Seq kit was used for sequencing library generation (Cat. Num.: PN 4445374). All steps were carried out according to the Manufacturer's instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
AB 5500xl Genetic Analyzer |
| |
|
| Description |
SeZ3_3
|
| Data processing |
CLC Genomics Workbench v 7.5.1.
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05).
Trimmed sequence reads were mapped to E. coli strain K-12 MG1655 / U00096.3 using CLC genomic benchwork (parameters- maximum number of mismatches: 2, minimum length: 0.8, similarity fractions: 0.8, unspecific match hit: 10)
Reads shorter than 50 bp were excluded.
Read count extraction were performed using CLC genomic benchwork.
Read count data were then imported into R version 3.0.249 excluding ribosomal DNA (rDNA) genes.
Assembly: U00096.3
Supplementary files format and content: Tab-delimited text files include raw gene counts for each Sample.
|
| |
|
| Submission date |
Jan 23, 2023 |
| Last update date |
Feb 03, 2023 |
| Contact name |
Gabor Grezal |
| E-mail(s) |
grezal.gabor@gmail.com
|
| Phone |
0036303063101
|
| Organization name |
Biological Research Centre
|
| Department |
Institute of Biochemistry
|
| Lab |
Balázs Papp Laboratory
|
| Street address |
Temesvári krt. 62.
|
| City |
Szeged |
| State/province |
Csongrád |
| ZIP/Postal code |
6701 |
| Country |
Hungary |
| |
|
| Platform ID |
GPL23187 |
| Series (1) |
| GSE223493 |
Plasticity and stereotypic rewiring of the transcriptome upon bacterial evolution of antibiotic resistance |
|
| Relations |
| BioSample |
SAMN32876219 |
| SRA |
SRX19142464 |
