Escherichia coli
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA288458 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR2080776.fastq.gz | Fastqsanger.gz |
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Project description:Study of the mechanisms of RecB mutant terminus DNA loss in Escherichia coli. FX158: WT MG1655 FX35: recB- FX37: ruvAB- FX51: matP- MIC18: recB- sbcD- sbcC- MIC20: recB- ruvAB- MIC24: matP- recB- MIC25: recA- recB- MIC31: sbcB- sbcD- MIC34: recA- recD- MIC40: linear chromosome MIC41: linear chromosome recB- MIC42: matP- ftsKC- MIC43: matP- ftsKC- recB- MIC48: recA- Cells were grown in M9 minimal medium supplemented with 0.4 % glucose to exponential phase (0.2 OD 650 nm). Chromosomal DNA was extracted using the Sigma GenElute bacterial genomic DNA kit. 5 μg of DNA were used to generate a genomic library according to Illumina's protocol. The libraries and the sequencing were performed by the High-throughput Sequencing facility of the I2BC (http://www.i2bc.paris-saclay.fr/spip.php?article399&lang=en, CNRS, Gif-sur-Yvette, France). Genomic DNA libraries were made with the ‘Nextera DNA library preparation kit’ (Illumina) following the manufacturer’s recommendations. Library quality was assessed on an Agilent Bioanalyzer 2100, using an Agilent High Sensitivity DNA Kit (Agilent technologies). Libraries were pooled in equimolar proportions. 75 bp single reads were generated on an Illumina MiSeq instrument, using a MiSeq Reagent kit V2 (500 cycles) (Illumina), with an expected depth of 217X. An in-lab written MATLAB-based script was used to perform marker frequency analysis. Reads were aligned on the Escherichia coli K12 MG1655 genome using BWA software. Data were normalized by dividing uniquely mapping sequence reads by the total number of reads. Enrichment of uniquely mapping sequence reads in 1 kb non-overlapping windows were calculated and plotted against the chromosomal coordinates.
2017-11-10 | E-MTAB-6122 | biostudies-arrayexpress
Project description:In past, resistance mechanisms have been identified by analysis of resistant isolates or defined mutants. Recently, high-throughput transposon mutagenesis coupled with sequencing (TraDIS-Xpress) is another approach proving useful for elucidating the roles of genes involved in the overall cellular response to a particular stress. In this study, we used TraDIS-Xpress to determine the role played by genes following exposure to colistin stress. Approximately 10^7 cells from the mutant library were inoculated into LB broth at a range of doubling concentrations of colistin ( 0.25 x MIC, 0.5 x MIC, 1 x MIC, 2 X MIC). Experiments were performed with no induction, or with induction using 0.2 or 1 mM of Isopropyl β-D-1-thiogalactopyranoside (IPTG). All experiments were performed in duplicate.
2022-06-09 | E-MTAB-11807 | biostudies-arrayexpress
Project description:Purpose: In this study, Escherichia coli DH5alpha whole transcriptome sequencing was performed in order to compare the different gene expression profiles between control and exposed to Wi-Fi radiofrequency radiations. Methods:Escherichia coli DH5alpha were exposed to Wi-Fi radiations. Total RNA samples( control and exposed ) were extracted by bacteria protect-Rneasy kit,treated with DNAase and subjected to sequnecing using an Illumina-NovaSeq 6000 platform. Library preparation and sequencing were performed by Macrogen (south korea).Trimmed reads are mapped to reference genome with Bowtie. HTseq was used for expression profiling. Expression profile was calculated for each sample and gene as read count.
2019-10-21 | GSE126584 | GEO
Project description:Purpose:In order to assess the respiratory toxicity of co-infection in chicken lung, we established a co-infection model to investigate transcriptome profiles of chicken lung. Methods: RNA extracted by Trizol reagent (Invitrogen) was utilized to construct the final library (BGISEQ-500 RNA-Seq Library) based on the manufacturer’s instructions. Library was validated on the Agilent Technologies 2100 bioanalyzer. The library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecule. The DNBs were load into the patterned nanoarray and single end 50 bases reads were generated in the way of sequenced by synthesis. Whole transcriptome sequencing data was filtered and mapped to Chicken genome (Gallus genome Version 5.0.1 NCBI). DEG-seq method was based on Poisson distribution (Fold Change > 2 and Adjusted P value < 0.001) Results: Sampling directly from the lung yielded sufficient quantities of RNA to assess transcripts from each chicken and mapped to 18,043 Gallus gallus genes. Conclusions: We used the method of RNA-seq to find the target genes and related signaling pathways involved in the co-infection (MG and E.coli) and their underlying mechanisms.
2019-04-19 | GSE130015 | GEO
Project description:E. coli terminator mutation library raw sequencing reads
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