|
| Status |
Public on May 31, 2019 |
| Title |
2905_B_t01_2 |
| Sample type |
SRA |
| |
|
| Source name |
t01_whole cell
|
| Organism |
Escherichia coli |
| Characteristics |
strain: BW25113
timepoint: t01
replicate: 2
sample type: whole cell
|
| Treatment protocol |
0.5 mL culture was transferred into reaction tubes and centrifuged at 11.000 rcf for 2 min, and the pellet was frozen in liquid nitrogen.
|
| Growth protocol |
E. coli BW25113 was cultivated in 1 L bioreactor with 500 mL of M9 minimal medium containing 5 g*L-1 glucose to an optical density at 600 nm (OD) of 2. Then the culture was centrifuged at 37 °C and 1800 rcf for 5 min. Pelleted cells were resuspended in M9 medium at 37°C without glucose and transferred back to the bioreactor. After 12 hours of starvation, 5 g*L-1 glucose was added again to the culture. Over this time course, total RNA was sampled. total RNA was sampled at different timepoints before starvation, during starvation and in the growth resumption phase. For detailed description of the sampling time points see Supplementary Material of the publication.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The total RNA of the cells was isolated using the Total RNA Isolation Mini Kit (Agilent, Santa Clara, CA).
Quality and Quantity of the extracted RNA were checked with a Agilent BioAnalyser. After an Ribosom depletion, the library was constructed using Directional RNAseq Library with NEBNext Ultra™ Directional RNA Library Prep Kit for Illumina (New England Biolabs).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
2905_B_run467_TGGTTGTT
|
| Data processing |
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Reads were aligned to the reference genome using the CLC Workbench Software (QIAGEN, Venlo, NL). TPMs were calculated using the same program
Genome_build: NC_000913
Supplementary_files_format_and_content: .csv file, exported from the analysis software CLC Workbench
|
| |
|
| Submission date |
May 30, 2019 |
| Last update date |
May 31, 2019 |
| Contact name |
Hannes Link |
| E-mail(s) |
hannes.link@synmikro.mpi-marburg.mpg.de
|
| Organization name |
MPI Marburg
|
| Department |
Dynamic Control of Metabolic Networks
|
| Lab |
Hannes Link
|
| Street address |
Karl-von-Frisch Straße 16
|
| City |
Marburg |
| State/province |
Hessen |
| ZIP/Postal code |
35043 |
| Country |
Germany |
| |
|
| Platform ID |
GPL26155 |
| Series (1) |
| GSE131992 |
Systematic identification of metabolites controlling gene expression in E. coli |
|
| Relations |
| BioSample |
SAMN11895613 |
| SRA |
SRX5936090 |
