|
Status |
Public on Mar 03, 2022 |
Title |
untreated Escherichia coli str. O157:H7 str. Sakai- replicate 2 |
Sample type |
SRA |
|
|
Source name |
untreated Escherichia coli str. O157:H7 str. Sakai
|
Organism |
Escherichia coli |
Characteristics |
serotype: O157:H7 strain: Sakai treatment: untreated (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 |
SAMN26226231 |
SRA |
SRX14276756 |