|
| Status |
Public on Sep 24, 2016 |
| Title |
log phase 3 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
untreated
|
| Organism |
Escherichia coli |
| Characteristics |
phase: log phase
strain: BW25113
|
| Treatment protocol |
Cells were grown in the absence and presence of 0.005 mg/mL 5-azacytidine to logarithmic phase (2 hours, A600=~0.45) or early stationary phase (8 hours, A600=~2.7)
|
| Growth protocol |
Escherichia coli cells were grown in LB at 37oC with shaking at 250 RPM
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated with the MasterPure RNA Isolation Kit (Epicentre), enriched for mRNA using the mRNA Prokaryotic mRNA Isolation Kit (Epicentre), and polyadenylated with kit all based on the manufacturer's instructions
|
| Label |
Cy3
|
| Label protocol |
Enriched RNA (0.5 mg) was converted to cRNA in the presence of Cy3-CTP or Cy5-CTP with the Quick Amp two-color labeling kit (Agilent) according to the manufacturer's instructions
|
| |
|
| Channel 2 |
| Source name |
5-azacytidine-treated
|
| Organism |
Escherichia coli |
| Characteristics |
phase: log phase
strain: BW25113
|
| Treatment protocol |
Cells were grown in the absence and presence of 0.005 mg/mL 5-azacytidine to logarithmic phase (2 hours, A600=~0.45) or early stationary phase (8 hours, A600=~2.7)
|
| Growth protocol |
Escherichia coli cells were grown in LB at 37oC with shaking at 250 RPM
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated with the MasterPure RNA Isolation Kit (Epicentre), enriched for mRNA using the mRNA Prokaryotic mRNA Isolation Kit (Epicentre), and polyadenylated with kit all based on the manufacturer's instructions
|
| Label |
Cy5
|
| Label protocol |
Enriched RNA (0.5 mg) was converted to cRNA in the presence of Cy3-CTP or Cy5-CTP with the Quick Amp two-color labeling kit (Agilent) according to the manufacturer's instructions
|
| |
|
| |
| Hybridization protocol |
Microarray slides were hybridized with 0.3 mg of both cRNAs for 17 hours at 65oC in 1x Agilent hybridization buffer in an Agilent rotisserie on setting 10, washed with Agilent GE wash buffers 1 and 2, and rinsed with acetonitrile
|
| Scan protocol |
Arrays were scanned on an Agilent G2505B or G2505C scanner; images were quantified using the Agilent Feature Extract Software (most recent version)
|
| Description |
biological replicate 3 of 5
|
| Data processing |
Agilent Feature Extract software performed background normalization and LOWESS correction for dye bias. Non-E. coli K-12 probes were removed from the dataset, as the BW25113 strain is a K-12 strain.
|
| |
|
| Submission date |
Oct 02, 2015 |
| Last update date |
Sep 24, 2016 |
| Contact name |
Kevin T Militello |
| E-mail(s) |
militello@geneseo.edu
|
| Phone |
585-245-5312
|
| Organization name |
State University of New York at Geneseo
|
| Department |
Biology
|
| Street address |
1 College Circle
|
| City |
Geneseo |
| State/province |
New York |
| ZIP/Postal code |
14454 |
| Country |
USA |
| |
|
| Platform ID |
GPL13360 |
| Series (1) |
| GSE73707 |
Escherichia coli: untreated versus 5-azacytidine-treated expression profiles |
|
