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Sample GSM2538646 Query DataSets for GSM2538646
Status Public on Mar 29, 2018
Title 25A
Sample type SRA
 
Source name chloramphenicol adapted line 9
Organism Escherichia coli
Characteristics strain: CHL9
resistance: CHL
treatment_protocol: CHL
Treatment protocol Control: the ancestor strain from which the antibiotic adaptation started.
AMP: Parallel lineages were adapted to gradually increasing concentrations of ampicillin for 30 transfers (around 240 generations).
CHL: Parallel lineages were adapted to gradually increasing concentrations of chloramphenicol for 48 transfers (around 384 generations).
CPR: Parallel lineages were adapted to gradually increasing concentrations of ciprofloxacin for 48 transfers (around 384 generations).
DOX: Parallel lineages were adapted to gradually increasing concentrations of doxycycline for 30 transfers (around 240 generations).
ERY: Parallel lineages were adapted to gradually increasing concentrations of erythromycin for 33 transfers (around 264 generations).
FOX: Parallel lineages were adapted to gradually increasing concentrations of cefoxitin for 48 transfers (around 384 generations).
KAN: Parallel lineages were adapted to gradually increasing concentrations of kanamycin for 45 transfers (around 360 generations).
NAL: Parallel lineages were adapted to gradually increasing concentrations of nalidixic acid for 48 transfers (around 384 generations).
NIT: Parallel lineages were adapted to gradually increasing concentrations of nitrofurantoin for 30 transfers (around 240 generations).
TET: Parallel lineages were adapted to gradually increasing concentrations of tetracycline for 39 transfers (around 312 generations).
TOB: Parallel lineages were adapted to gradually increasing concentrations of tobramycin for 45 transfers (around 360 generations).
TRM: Parallel lineages were adapted to gradually increasing concentrations of trimethoprim for 36 transfers (around 288 generations).
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 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
 
Data processing Basecalls were performed using Abi Solid 5 ICS
Data was filtered based on read length. Minimum number of nucleotides in reads = 50, Software: CLC Genomics Workbench Tool 7.5.1
CLC Legacy RNA-Seq analysis was carried out. Min. length fraction = 0.8, Min. similarity fraction = 0.8, Additional upstream bases = 0, Additional downstream bases = 0, Maximum number of mismatches allowed (applies to short reads) = 2, Unspecific match limit = 10, Use colorspace encoding = Yes, Use strand specific assembly = No, Organism type = PROKARYOTE, Exon discovery = Yes, Minimum number of reads = 10, Minimum length of putative exons = 50, Create list of unmapped reads = No, Create report = Yes, Create fusion gene table = No, Expression level = Genes, Calculate RPKM for genes without transcripts = No, Expression value = Number of reads mapped to the gene, Software: CLC Genomics Workbench Tool 7.5.1
rRNA reads were discarded
Genes unexpressed in the majority of samples were removed (expression threshold: at least 5 read counted in at least 21 samples)
TMM scale normalization was used. Function: calcNormFactors, Package: edgeR, Version 3.4.2
Voom log2 transformation together with quantile normalization was applied. Function: voom normalize=quantile, Package: limma, Version: 3.18.13
Batch effect removal was applied using non-treated controls samples as reference points. Function:ComBat, Package: sva, version: 3.8.0
linear modeling with empirical Bayes moderation was built in limma. Package: limma, Version: 3.18.13
Genome_build: U00096.3 annoted with Blatner locus numbers, downloaded from EcoGene 3.0
Supplementary_files_format_and_content: Comma separated files containing RNA-Seq count data, exported from CLC Genomics Workbench Tool
 
Submission date Mar 16, 2017
Last update date May 15, 2019
Contact name Balazs Balint
E-mail(s) balintb@seqomics.hu
Phone 0036304276152
Organization name Seqomics Ltd
Street address Vallalkozok street
City 7
State/province Csongrad
ZIP/Postal code 6782
Country Hungary
 
Platform ID GPL23187
Series (1)
GSE96706 Collateral sensitivity of antibiotic resistant bacteria to antimicrobial peptides
Relations
BioSample SAMN06607525
SRA SRX2646876

Supplementary file Size Download File type/resource
GSM2538646_25A.RNA_Seq.counts.csv.gz 71.4 Kb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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