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Status |
Public on Mar 29, 2018 |
Title |
8C |
Sample type |
SRA |
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Source name |
tobramycin adapted line 9
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Organism |
Escherichia coli |
Characteristics |
strain: TOB9 resistance: TOB treatment_protocol: TOB
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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).
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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.
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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.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
AB 5500xl Genetic Analyzer |
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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
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Submission date |
Mar 16, 2017 |
Last update date |
May 15, 2019 |
Contact name |
Balazs Balint |
E-mail(s) |
balintb@seqomics.hu
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Phone |
0036304276152
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Organization name |
Seqomics Ltd
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Street address |
Vallalkozok street
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City |
7 |
State/province |
Csongrad |
ZIP/Postal code |
6782 |
Country |
Hungary |
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Platform ID |
GPL23187 |
Series (1) |
GSE96706 |
Collateral sensitivity of antibiotic resistant bacteria to antimicrobial peptides |
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Relations |
BioSample |
SAMN06607539 |
SRA |
SRX2646860 |
Supplementary file |
Size |
Download |
File type/resource |
GSM2538630_8C.RNA_Seq.counts.csv.gz |
71.2 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
Processed data are available on Series record |
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