|
| Status |
Public on Mar 03, 2022 |
| Title |
bicyclomycin treated Escherichia coli str. O157:H7 str. Sakai- replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
bicyclomycin treated Escherichia coli str. O157:H7 str. Sakai
|
| Organism |
Escherichia coli |
| Characteristics |
serotype: O157:H7
strain: Sakai
treatment: bicylomycin treated (15 minutes) at OD600 = 0.6
|
| Treatment protocol |
At an OD600 of 0.6, cultures were split into two, with half being treated with 50 μg/mL of bicyclomycin
|
| Growth protocol |
Three individual colonies were grown in MEM-HEPES supplemented with 0.1% glucose and 250 nM ferric nitrate
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using guanidinium thiocyanate phenol as in (Tollervery & Mattaj 1987)
RNA was depleted with Zymo-seq RiboFree Total RNA kit before library prep for sequencing on the NextSeq paired end flow cell
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
grown to OD600 of 0.6 in MEM-HEPES supplemented with 0.1% glucose and 250 nM Fe(NO3)3
|
| Data processing |
Differentially expressed genes were determined using READemption 1.01 (PMID: 25123900)
Rho scores were derived from RNA-seq data using the pipeline from PMID: 33460557
Genome_build: NC_002695.2
Supplementary_files_format_and_content: Differentially expressed gene in CSV table. Predicted Rho termination sites in TEXT table
|
| |
|
| Submission date |
Feb 24, 2022 |
| Last update date |
Mar 03, 2022 |
| Contact name |
Jai Justin Tree |
| E-mail(s) |
j.tree@unsw.edu.au
|
| Phone |
+61 2 938 59142
|
| Organization name |
University of New South Wales
|
| Department |
School of Biotechnology and Biomolecular Sciences
|
| Lab |
Tree lab
|
| Street address |
Rm s110 Bldg F25, UNSW, Gate 11 Botany St
|
| City |
Sydney |
| State/province |
NSW |
| ZIP/Postal code |
2033 |
| Country |
Australia |
| |
|
| Platform ID |
GPL21222 |
| Series (1) |
| GSE197379 |
RNA-sequencing of bicyclomycin treated Escherichia coli str. O157:H7 str. Sakai |
|
| Relations |
| BioSample |
SAMN26226234 |
| SRA |
SRX14276753 |
