|
| Status |
Public on Jul 31, 2022 |
| Title |
Control OD= 0.5 rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Escherichia coli BW25113
|
| Organism |
Escherichia coli |
| Characteristics |
strain: BW25113 WT
treatment: Control
time-point: OD 600= 0.5
|
| Treatment protocol |
Bacterial pellets were treated with LP-600 at the concentration of 0.0625, 128 µg/ml or DMSO as vehicle control and were harvested at OD 600= 0.5 or 1.0.
|
| Growth protocol |
Overnight cultures were grown in iron-limited MHB medium at 37 °C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted by applying the RNAeasy Mini Kit (Qiagen cat. 74104) and followed by the DNase treatment (Qiagen cat. 79254). Total RNA quality and integrity were assessed using the 5200 Fragment Analyzer System (Agilent Technologies). By applying NEBNext® Ultra™ II Directional RNA Library Prep Kit (New England BioLabs), total RNA library was generated from 1 mg total RNA after rRNA depletion through Ribo-off rRNA Depletion Kit (Bacteria) (Vazyme BioTech Co.Ltd.).
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Raw reads were saved in FASTQ format. Quality control and adapter clipping were done using fastq-mcf tool of ea-utils
Sequenced reads were then mapped to whole genome of E. coli strain BW25113 (genebank: CP009273.1)using Rockhopper
The raw counts of reads were normalized differential expression analysis were performed with the R package-limma (version 3.42.2)
Genome_build: E. coli BW25113
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
|
| |
|
| Submission date |
Mar 03, 2022 |
| Last update date |
Jul 31, 2022 |
| Contact name |
Yi-Hui Lai |
| Organization name |
Helmholtz Centre for Infection Research
|
| Street address |
Inhoffenstr. 7
|
| City |
Braunschweig |
| ZIP/Postal code |
38124 |
| Country |
Germany |
| |
|
| Platform ID |
GPL25368 |
| Series (1) |
| GSE197880 |
Molecular signatures of the Eagle effect induced by the artificial siderophore conjugate LP-600 in E. coli |
|
| Relations |
| BioSample |
SAMN26419716 |
| SRA |
SRX14360568 |
