|
| Status |
Public on Apr 28, 2016 |
| Title |
rpoB_546_M9 |
| Sample type |
SRA |
| |
|
| Source name |
rpoBE546V mutant
|
| Organism |
Escherichia coli str. K-12 substr. MG1655 |
| Characteristics |
genotype/variation: rpoBE546V mutant
media: M9 minimal
growth mode: Batch
carbon source: glucose
|
| 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
Ribosomal RNA was substracted and dUTP method was used for library preparation
|
| |
|
| 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: NC_000913.2
Supplementary_files_format_and_content: .txt files with fpkm values of each condition
|
| |
|
| Submission date |
Jul 14, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Jose Utrilla |
| E-mail(s) |
[email protected]
|
| Organization name |
Universidad Nacional Autonoma de México
|
| Department |
Centro de Ciencias Genómicas
|
| Street address |
Av. Universidad sn
|
| City |
Cuernavaca |
| State/province |
Morelos |
| ZIP/Postal code |
62210 |
| Country |
Mexico |
| |
|
| Platform ID |
GPL17439 |
| Series (1) |
| GSE59377 |
Global Rebalancing of Cellular Resources by Pleiotropic Point Mutations Illustrates a Multi-scale Mechanism of Adaptive Evolution |
|
| Relations |
| BioSample |
SAMN02911311 |
| SRA |
SRX651941 |
