|
| Status |
Public on Oct 10, 2015 |
| Title |
sigD4_T |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
wildtype
|
| Organism |
Bacillus subtilis |
| Characteristics |
strain: PY79
genotype/variation: wildtype
|
| 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
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
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 |
sigD::tet
|
| Organism |
Bacillus subtilis |
| Characteristics |
strain: PY79
genotype/variation: sigD::tet
|
| 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
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
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.
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
Agilent Technologies DNA Microarray Scanner with Surescan High-Resolution Technology
|
| Description |
SigD regulon Replicate 4: A wild-type PY79 and sigD mutant (PE2597) cultures were grown in parallel in Difco Sporulation Medium. Samples were collected during late-log (LL), and transition to stationary phase (T),
|
| 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.
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 |
Oct 09, 2015 |
| Last update date |
Oct 10, 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. |
|
