|
| Status |
Public on Aug 23, 2022 |
| Title |
IR_BW25113_M9_Glc_Thr6_R1 |
| Sample type |
SRA |
| |
|
| Source name |
Exp_BW25113 E. coli, M9 medium, L-Thr added_1
|
| Organism |
Escherichia coli BW25113 |
| Characteristics |
genotype: WT
|
| Treatment protocol |
Cells were treated with the Qiagen RNA-protect bacterial reagent according to the manufacturer’s specifications.
|
| Growth protocol |
RNA sequencing data were generated under aerobic exponential growth conditions in M9 medium supplemented with 6mM L-threonine. The wild type BW25113 strain was grown as a control for the isogenic mutant strain. Pre-cultures for the RNA sequencing experiments were taken by scraping frozen stocks and growing the cells in LB medium. Cells were washed twice with M9 medium and inoculated at an OD600 of 0.05. The cells were collected at an OD600 of 0.9 (only ycaN, yiaU, ybhD mutants and WT control collected at OD600 of 2.2 for late-exponential phase)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Pelleted cells were stored at -80oC, and after cell resuspension and partial lysis, they were ruptured with a beat beater; the total RNA was extracted using a Qiagen RNA purification kit.
Paired-end RNA-Seq libraries were constructed using a KAPA RNA HyperPrep kit from Kapa Biosystems (Wilmington, MA, USA).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
IR_BW25113_M9_Glc_Thr6_R1
|
| Data processing |
Raw RNA-Seq reads were mapped to the original reference genome using Bowtie2 and transcript abundance was analyzed using summarizeOverlaps (Lawrence et al., 2013). Calculation of transcripts per million (TPM) and prediction of differentially expressed genes were conducted using DESeq2 (Love et al., 2014).
|
| |
|
| Submission date |
Aug 24, 2021 |
| Last update date |
Aug 23, 2022 |
| Contact name |
Bernhard O. Palsson |
| Organization name |
University of California, San Diego
|
| Department |
Bioengineering
|
| Lab |
Systems Biology Research Group
|
| Street address |
9500 Gilman Dr
|
| City |
San Diego |
| State/province |
California |
| ZIP/Postal code |
92093 |
| Country |
USA |
| |
|
| Platform ID |
GPL27123 |
| Series (1) |
| GSE182695 |
Systems approach for identification of the Escherichia coli K-12 LysR-type transcriptional regulators function. |
|
| Relations |
| BioSample |
SAMN20962176 |
| SRA |
SRX11897682 |
