|
| Status |
Public on Jan 05, 2023 |
| Title |
Δnac glutamine 2 (RNA-seq) |
| Sample type |
SRA |
| |
|
| Source name |
bacteria cells
|
| Organism |
Escherichia coli K-12 |
| Characteristics |
strain: MG1655
nitrogen source: glutamine
genotype: delta nac
phase: mid-log phase
medium: W2 minimal media
|
| Treatment protocol |
The cell culture was treated with the RNAprotect reagent (Qiagen).
|
| Growth protocol |
E. coli K-12 MG1655 nac and ntrC mutant cells were 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 Qubit 4.0 (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 |
NextSeq 550 |
| |
|
| 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 |
Jun 07, 2022 |
| Last update date |
Jan 05, 2023 |
| Contact name |
Donghyuk Kim |
| E-mail(s) |
dkim@unist.ac.kr
|
| 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 |
GPL26204 |
| 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 |
SAMN28902457 |
| SRA |
SRX15625732 |
