|
| Status |
Public on Aug 01, 2018 |
| Title |
N_p3 |
| Sample type |
SRA |
| |
|
| Source name |
WT strain
|
| Organism |
Escherichia coli str. K-12 substr. MG1655 |
| Characteristics |
growth mode: Chemostat
growth rate (hour^-1): 0.3
growth limitation: Ammonium
media: M9 minimal
|
| Treatment protocol |
Samples were taken with 2 volumes of RNAprotect reagent (quiagen)
|
| Growth protocol |
Cultures were grown in batch or chemostat mode, M9 minimal media or LB complex media. Samples for Batch mode were taken from mid-log phase, samples from chemostat were taken once the steady state was achieved
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted by cell lysis followed by column purification and DNAse treatment. RNA-seq was performed following a modified dUTP method (PMID: 23637642). The rRNA was isolated using Epicentre's Ribo-Zero rRNA removal kit for Gram Negative Bacteria.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina MiSeq |
| |
|
| Data processing |
Alignment with Bowtie1.
The obtained reads were mapped to the E. coli MG1655 genome (NC_000913.2) using the short-read aligner Bowtie 25 with two mismatches allowed per read alignment.
To estimate gene expression FPKM values were calculated using cufflinks tool 2.0.2
Genome_build: ASM584v1 (NC_000913.2)
Supplementary_files_format_and_content: tab-delimited .txt files with fpkm values of each condition
|
| |
|
| Submission date |
Aug 12, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Edward OBrien |
| E-mail(s) |
[email protected]
|
| Organization name |
UCSD
|
| Street address |
417 Powell-Focht Bioengineering Hall, 9500 Gilman Drive La Jolla
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093 |
| Country |
USA |
| |
|
| Platform ID |
GPL17439 |
| Series (1) |
| GSE72020 |
Proteome allocation constraints determine cellular growth rates and demand fitness trade-offs |
|
| Relations |
| BioSample |
SAMN03988209 |
| SRA |
SRX1144222 |
