|
| Status |
Public on Mar 20, 2015 |
| Title |
Com2_T+1.5 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
reference
|
| Organism |
Bacillus subtilis |
| Characteristics |
strain: PY79
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the Hot Phenol method followed by Dnase treatment and cleaning with Qiagen's Rneasy kit
|
| Label |
cy3
|
| Label protocol |
6-10 ug of RNA was labelled using Agilent's Fairplay III Protocol for NHS-ester dye-coupling reaction to amino allyl dUTP . Cy3 and Cy5 were purchased from GE Healthcare
|
| |
|
| Channel 2 |
| Source name |
sample
|
| Organism |
Bacillus subtilis |
| Characteristics |
strain: PY79
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the Hot Phenol method followed by Dnase treatment and cleaning with Qiagen's Rneasy kit
|
| Label |
cy5
|
| Label protocol |
6-10 ug of RNA was labelled using Agilent's Fairplay III Protocol for NHS-ester dye-coupling reaction to amino allyl dUTP . Cy3 and Cy5 were purchased from GE Healthcare
|
| |
|
| |
| Hybridization protocol |
Hybridizations were incubated at 65˚C for 17 hours. After hybridization slides were washed using Agilent's Wash Buffer 1 and 2.
|
| Scan protocol |
Agilent Technologies DNA Microarray Scanner with Surescan High-Resolution Technology
|
| Description |
Competence medium Replicate 2: A wild-type PY79 culture was grown in Competence Medium and samples were collected at 1.5 (OD600nm 0.4), 1 (OD600nm 0.4), and 0.5 (OD600nm 0.6) hours before the onset of stationary phase, the onset of stationary phase (OD600nm 0.9), and 0.5 (OD600nm 0.9), 1.5 (OD600nm 1.0), 2.5 (OD600nm 0.9), and 3.5 (O.D.600nm 1.0) hours after the onset of stationary phase. A common reference was made by pooling RNA from each time point.
|
| Data processing |
Microarray data processing was performed in R (www.r-project.org) using the Bioconductor bioinformatics software package (www.bioconductor.org). Data were loaded into R using the marray package and normalized between arrays using loess normalization. Normalized log-ratios of gMedianSignal and rMedianSignal were collapsed for redundant probes taking the average.
|
| |
|
| Submission date |
Mar 18, 2015 |
| Last update date |
Oct 09, 2015 |
| Contact name |
Patrick Eichenberger |
| E-mail(s) |
[email protected], [email protected]
|
| Organization name |
New York University
|
| Department |
Center for Genomics and Systems Biology
|
| Lab |
Eichenberger
|
| Street address |
12 Waverly Place
|
| City |
New York |
| State/province |
New York |
| ZIP/Postal code |
10003 |
| Country |
USA |
| |
|
| Platform ID |
GPL15179 |
| Series (1) |
| GSE67023 |
An experimentally supported model of the Bacillus subtilis global transcriptional regulatory network. |
|
