 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Mar 29, 2018 |
| Title |
62A |
| Sample type |
SRA |
| |
|
| Source name |
nitrofurantoin adapted line 7
|
| Organism |
Escherichia coli |
| Characteristics |
strain: NIT7
resistance: NIT
treatment_protocol: NIT
|
| 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) |
[email protected]
|
| 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 |
SAMN06607567 |
| SRA |
SRX2646918 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2538688_62A.RNA_Seq.counts.csv.gz |
71.8 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 |
|
|
|
|
 |
