|
| Status |
Public on Jul 10, 2014 |
| Title |
Sample 53b |
| Sample type |
SRA |
| |
|
| Source name |
CIP_25_BR2
|
| Organism |
Acinetobacter sp. 1592897 |
| Characteristics |
sample name: CIP_25_BR2
agent: ciprofloxacin
dose: 25% of approximate MIC
|
| Treatment protocol |
Once they reached an OD600 of 0.4, the cultures to receive antibiotic treatment were amended with 25% or 75% of the approximate MIC value of one antibiotic (meropenem, ciprofloxacin, amikacin sulfate, or polymyxin-B), then they were incubated for 15 min at 37˚C with shaking (225 rpm). The no treatment controls grown in regular MHB, and also the MHB + 200 mM NaCl treatment, were not amended with antibiotic and were incubated for an additional 15 min after reaching an OD600 of 0.4.
|
| Growth protocol |
Acinetobacter strains were inoculated 1:100 from overnight cultures and grown to an OD600 of approximately 0.4 in Mueller Hinton Broth (MHB), or MHB supplemented with 200mM NaCl, at 37˚C with shaking (225 rpm)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The cells were pelleted from the media by pelleting at 5,000 x g for 5 min, and total RNA was extracted using the Ambion RiboPure Bacteria kit. The RNA was treated with the Ribopure DNase I, and the rigorous treatment using the Turbo DNA-free kit to remove contaminating DNA.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Base calls were performed using the bulit in Illumina basecaller.
Sequenced reads were mapped to the Acinetobacter baumannii genome using Bowtie v. 0.12.9
RPKM values were calculated for the genes present in the Acinetobacter baumannii genome.
Genome_build: Acinetobacter baumanni 1592897 ASM58231v1
Supplementary_files_format_and_content: Tab-delimted files report RPKM values.
|
| |
|
| Submission date |
Jul 10, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
David A Rasko |
| E-mail(s) |
drasko@som.umaryland.edu
|
| Phone |
410 706 6774
|
| Organization name |
University of Maryland School of Medicine
|
| Department |
Istitute for Genome Sciences/Microbiology and Immunology
|
| Street address |
801 W. Baltimore Street, Room 619
|
| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21201 |
| Country |
USA |
| |
|
| Platform ID |
GPL18925 |
| Series (2) |
| GSE56217 |
Examination of the transcirptional response of Acinetobacter baumannii to antibiotics |
| GSE56226 |
RNA-seq in response to antibiotic stress (Acinetobacter baumannii 1592897) |
|
| Relations |
| SRA |
SRX483014 |
| BioSample |
SAMN02677666 |
