|
| Status |
Public on Mar 20, 2015 |
| Title |
DSM1_T-1.0 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| 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 |
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 |
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 |
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 |
Growth and sporulation in DSM Replicate 1: A wild-type PY79 culture was grown in Difco Sporulation Medium. Samples were taken at 1.5 (OD600nm 1.0), 1 (OD600nm 1.3), and 0.5 (OD600nm 1.7) hours before the onset of stationary phase, the onset of stationary phase (OD600nm 1.9), and 0.5 (OD600nm 1.9), 1 (OD600nm 2.3), 1.5 (OD600nm 2.2), 2.5 (OD600nm 2.3), 3.5 (OD600nm 2.0), 4 (OD600nm 2.3), 4.5 (OD600nm 2.6), 5 (OD600nm 2.7), and 5.5 (OD600nm 2.9) 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) |
pe19@nyu.edu, arb401@nyu.edu
|
| 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. |
|
