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Sample GSM1432571 Query DataSets for GSM1432571
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

Supplementary file Size Download File type/resource
GSM1432571_1592897_CIP_25_BR2.bowtie.sorted_by_position.genic.coverage.stats.rpkm.txt.gz 107.0 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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