|
| Status |
Public on Jun 09, 2017 |
| Title |
ΔompR NaCl 1 |
| Sample type |
SRA |
| |
|
| Source name |
Total RNA isolated from E. coli
|
| Organism |
Escherichia coli str. K-12 substr. MG1655 |
| Characteristics |
strain: K-12 MG1655
genotype: ompR deletion mutant
|
| Treatment protocol |
The cell culture was treated with the RNAprotect reagent (Qiagen).
|
| Growth protocol |
E. coli K-12 MG1655 WT and ΔompR were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose. Then cells were treated with 0.3 M of NaCl at mid-log pahse for 30 min with agitation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the RNeasy Plus Mini kit (Qiagen Inc., Valencia, CA, USA) and genomic DNA was removed by gDNA Eliminator spin column in the RNeasy Plus Mini Kit. RNA quality and concentration was determined by analysis with a NanoDrop 1000 (Thermo Scientific Inc., Wilmington, DE, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina MiSeq |
| |
|
| Data processing |
Sequenced reads were mapped onto NC_000913 reference genome sequence using bowtie v1.0.0 with parameters -X 1000 -n 2 -3 3 -S
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using cufflinks v.1.3.0
Genome_build: NC_000913
Supplementary_files_format_and_content: comma-delimited text files include FPKM values for each Sample.
|
| |
|
| Submission date |
Oct 20, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Donghyuk Kim |
| E-mail(s) |
[email protected]
|
| Organization name |
UNIST
|
| Department |
Department of Chemical Engineering
|
| Lab |
Systems Biology Lab
|
| Street address |
50 UNIST-gil, Eonyang-eup, Ulju-gun
|
| City |
Ulsan |
| ZIP/Postal code |
44919 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL17439 |
| Series (2) |
| GSE88980 |
Revealing the genome-scale transcriptional regulatory landscape of OmpR highlights its expanded regulatory roles and unexpected importance of narU under osmotic stress in Escherichia coli K-12 MG1655 [RNA-seq] |
| GSE88981 |
Revealing the genome-scale transcriptional regulatory landscape of OmpR highlights its expanded regulatory roles and unexpected importance of narU under osmotic stress in Escherichia coli K-12 MG1655 |
|
| Relations |
| BioSample |
SAMN05930265 |
| SRA |
SRX2254714 |
