|
| Status |
Public on Mar 25, 2017 |
| Title |
RNA-seq 37C LB rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Escherichia coli str. K-12 substr. MG1655
|
| Organism |
Escherichia coli str. K-12 substr. MG1655 |
| Characteristics |
cell type: Escherichia coli str. K-12 substr. MG1655
|
| Treatment protocol |
No treatment
|
| Growth protocol |
Glycerol stocks of E. coli K12 strain MG1655 were inoculated into LB media grown at 37 ℃ with constant agitation overnight. Cultures were diluted 1:100 into fresh minimal medium and then cultured at 37 ℃ to mid-exponential phase (OD600 nm ~ 0.6).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
From the cells cultured in LB media at 37 ℃, total RNA was extracted using RNAsnapTM method, followed by the ethanol precipitation. rRNA was removed using ribo-zeroTM magnetic kit for bacteria in accordance with manufacturer’s instruction (Epicentre). rRNA removal was confirmed using ExperionTM system. Subsequently, 4 µg of the purified RNA was fragmented to sizes of ~300 bp using RNA fragmentation reagent (Ambion, Grand Island, NY).
50 ng of the fragmented RNA was converted to sequencing library using TruSeq® Stranded mRNA Sample Prep Kit in accordance with manufacturer’s instruction (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina MiSeq |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.4
All sequencing reads were mapped to E. coli MG1655 reference genome (NC_000913) using CLC Genomics Workbench5 with the length fraction of 0.9 and the similarity of 0.99.
The expression levels were based upon the RPKM metric obtained from strand-specific manner.
Supplementary_files_format_and_content: RPKM is generated by in-house script
|
| |
|
| Submission date |
Mar 24, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Byung-Kwan Cho |
| Organization name |
KAIST
|
| Lab |
Systems and Synthetic Biology Lab
|
| Street address |
291 Daehak-ro
|
| City |
Daejeon |
| ZIP/Postal code |
305-701 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL17439 |
| Series (1) |
| GSE67218 |
Transcriptional expression level of E. coli at 37 ℃ in LB media |
|
| Relations |
| BioSample |
SAMN03444667 |
| SRA |
SRX966753 |
