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| Status |
Public on Jun 21, 2024 |
| Title |
24h amp media rep2 |
| Sample type |
SRA |
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| Source name |
bacterial cell
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| Organism |
Escherichia coli |
| Characteristics |
cell type: bacterial cell
strain: DH5alphaZ1
plasmid: p24KmNB82
treatment: ampicillin (24h)
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| Treatment protocol |
Stationary phase cultures were diluted 1/100 into fresh MMB+ media and collected after 24 h . Ampicillin treated cultures also contained 0.1 mg/mL ampicillin. Cip treatment at a concentration of 10 μg/mL for 6 h.
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| Growth protocol |
Cultures were grown in modified MMB+ media, which consists of the following: K2HPO4 (10.5 mg/ml), KH2PO4 (4.5 mg/ml), (NH4)2SO4 (2.0 mg/ml), C6H5Na3O7 (0.5 mg/ml), NaCl (1.0 mg/ml), 2 mM MgSO4 x 7H2O, 100 µM CaCl2, thiamine (10 µg/ml), 0.5% glycerol, amino acids (40 µg/ml) and kanamycin (25 µg/ml)
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| Extracted molecule |
total RNA |
| Extraction protocol |
Samples were treated with Tween (0.2%) and chloramphenicol (5 µg/ml) then immediately filtered out of solution and resuspended in lysis buffer containing 25 mM Tris pH 8.0, 25 mM NH4Cl, 10 mM MgOAc, 0.8 % Triton X-100, 0.1 U/µL RNase-free DNase I, 1 U/μL. Then immediately frozen in liquid nitrogen and stored at -80 C. Frozen pellets were thawed on ice and centrifuged for 20 minutes at 16,000 x g at 4 °C with 0.3% Sodium Deoxychorate to pellet particulate matter. The supernatant was then removed and RNA was column purified (Qiagen miRNeasy cat. No. 217004) before removing rRNA (Invitrogen RiboMinus cat no. K155004) Superase-In, ~60 U/µl ReadyLyse Lysozyme, 1.55 mM Chloramphenicol, and 17 μΜ 5′-guanylyl imidodiphosphate (GMPPNP).
cDNA libraries were prepared and multiplexed according to manufacturer's protocols: NEBNext Ultra II cat no. E7103S. Libraries were then pooled and sequenced by Illumina HiSeq paired-end sequencing.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Fastq files were aligned to NC_000913.3 and the plasmid p24KmNB82 using Geneious v. 2022.0.2
Raw read counts were calculated using 'calculate expression tool' in Geneious v. 2022.0.2
Assembly: NC_000913.3
Supplementary files format and content: Table with raw read counts for every gene and sample; comma separated values
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| Submission date |
Feb 20, 2024 |
| Last update date |
Jun 21, 2024 |
| Contact name |
Nicholas C Butzin |
| E-mail(s) |
nicholas.butzin@gmail.com
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| Phone |
6056884078
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| Organization name |
South Dakota State University
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| Department |
Biology and Microbiology
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| Lab |
Butzin Lab
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| Street address |
1224 Medary Ave.
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| City |
Brookings |
| State/province |
SD |
| ZIP/Postal code |
57007 |
| Country |
USA |
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| Platform ID |
GPL14548 |
| Series (1) |
| GSE256167 |
An isogenic E. coli population gives rise to multiple persister phenotypes |
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| Relations |
| SRA |
SRX23644786 |
| BioSample |
SAMN39964666 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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