|
| Status |
Public on Mar 15, 2012 |
| Title |
Calibration experiment (#1-1) of wild type and nifA mutant |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
wild type and nifA mutant (Cy3)
|
| Organism |
Rhodopseudomonas palustris |
| Characteristics |
sample type: mixed RNA from wild-type and nifA mutant cells
growth: NF with succinate and yeast extract
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Rhodopseudomonas palustris cells were disrupted by bead beating and RNA was purified with the RNeasy Mini kit (Qiagen) including DNase treatment on the column.
|
| Label |
Cy3
|
| Label protocol |
Fluorescently labeled cDNA was prepared by direct incorporation of either Cy3-dCTP or Cy5-dCTP during a first-strand reverse transcription reaction.
|
| |
|
| Channel 2 |
| Source name |
wild type and nifA mutant (Cy5)
|
| Organism |
Rhodopseudomonas palustris |
| Characteristics |
sample type: mixed RNA from wild-type and nifA mutant cells
growth: NF with succinate and yeast extract
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Rhodopseudomonas palustris cells were disrupted by bead beating and RNA was purified with the RNeasy Mini kit (Qiagen) including DNase treatment on the column.
|
| Label |
Cy5
|
| Label protocol |
Fluorescently labeled cDNA was prepared by direct incorporation of either Cy3-dCTP or Cy5-dCTP during a first-strand reverse transcription reaction.
|
| |
|
| |
| Hybridization protocol |
The hybridization mixtures containing the two labeled cDNA samples to be compared were applied to microarray slides that had been covered with Lifterslips (Erie Scientific Company, Portsmouth, NH). The slides were assembled with hybridization chambers (Corning, Corning, NY) and submerged in a 65ºC water bath for 14-16 h of hybridization.
|
| Scan protocol |
After hybridization, the slides were washed and scanned with a scanner from PerkinElmer or Agilent.
|
| Data processing |
Images (Cy3 and Cy5) were captured as TIFF files and were analyzed with the image processing software ImaGene version 5.6 (BioDiscovery, Inc., El Segundo, CA).
|
| |
|
| Submission date |
Sep 19, 2011 |
| Last update date |
Mar 15, 2012 |
| Contact name |
Yasuhiro Oda |
| E-mail(s) |
yasuhiro@uw.edu
|
| Organization name |
University of Washington
|
| Department |
Department of Microbiology
|
| Lab |
Harwood
|
| Street address |
Box 357242, 1705 N.E. Pacific Street, HSB K-354
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98195-7242 |
| Country |
USA |
| |
|
| Platform ID |
GPL2697 |
| Series (1) |
| GSE32292 |
How post-translational modification of nitrogenase is circumvented in Rhodopseudomonas palustris strains that produce hydrogen gas constitutively |
|
