|
| Status |
Public on Jan 05, 2023 |
| Title |
ammonia 1 (RNA-Seq) |
| Sample type |
SRA |
| |
|
| Source name |
Total RNA isolated from E. coli
|
| Organism |
Escherichia coli str. K-12 substr. MG1655 |
| Characteristics |
nitrogen source: ammonia
genotype/variation: WT
|
| Treatment protocol |
The cell culture was treated with the RNAprotect reagent (Qiagen).
|
| Growth protocol |
E. coli K-12 MG1655 WT was grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose, or W2 minimal media with 0.2% glucose and 2 g/L glutamine, cytidine or cytosine.
|
| 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
Transcripts Per kilobase Megabase of library size (TPM) were calculated using DEseq2.0
Assembly: NC_000913.2
Supplementary files format and content: comma-delimited text files include TPM values for each Sample.
|
| |
|
| Submission date |
Feb 12, 2014 |
| Last update date |
Jan 05, 2023 |
| 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) |
| GSE54904 |
Elucidating transcriptional regulation of nitrogen metabolism with systems approaches [RNA-Seq] |
| GSE54905 |
Elucidating transcriptional regulation of nitrogen metabolism with systems approaches |
|
| Relations |
| BioSample |
SAMN02640351 |
| SRA |
SRX469890 |
