|
| Status |
Public on Sep 12, 2008 |
| Title |
100 ng rbcL from ST-108 |
| Sample type |
mixed |
| |
|
| Channel 1 |
| Source name |
particulate material from ~4 L of surface seawater
|
| Organism |
uncultured organism |
| Characteristics |
100 ng of rbcL PCR target prepared from DNA extacted from sample ST-108
phytoplankton
Sample collected August 2004
|
| Treatment protocol |
Water was filtered onto 0.2 µm sterivex filters and immediately frozen at -80oC until extraction
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted using the Gentra PureGene cell culture protocol (Qigen); RNA was extracted using the RNAqueous kit (Ambion)
|
| Label |
Cy3
|
| Label protocol |
Targets were linearly ampified using Klenow and the dNTP mix included dUaa. The amplified product was post labeled by conjugation of Cy3 to the dUaa
|
| |
|
| Channel 2 |
| Source name |
20-mer standard reference
|
| Organism |
unidentified |
| Characteristics |
internal oligo reference
|
| Treatment protocol |
Water was filtered onto 0.2 µm sterivex filters and immediately frozen at -80oC until extraction
|
| Extracted molecule |
other |
| Extraction protocol |
DNA was extracted using the Gentra PureGene cell culture protocol (Qigen); RNA was extracted using the RNAqueous kit (Ambion)
|
| Label |
Cy5
|
| Label protocol |
Targets were linearly ampified using Klenow and the dNTP mix included dUaa. The amplified product was post labeled by conjugation of Cy3 to the dUaa
|
| |
|
| |
| Hybridization protocol |
hybridization at 55 or 65 oC using Contech hybridization solution
|
| Scan protocol |
Affymetrix 418 scanner with GMS Scanner Software Version 1.51.0.42
|
| Description |
Each feature contains a 90-mer, 70-mer of which is a specific probe for one of the functional genes of interest, and 20-mer of which is a standard reference.
|
| Data processing |
ImaGene 5.6.1 software and excel data filtering
|
| |
|
| Submission date |
Sep 11, 2008 |
| Last update date |
Sep 11, 2008 |
| Contact name |
Bess B Ward |
| E-mail(s) |
bbw@princeton.edu
|
| Phone |
6092585150
|
| Fax |
6092580796
|
| Organization name |
Princeton University
|
| Department |
Geosciences
|
| Lab |
Ward
|
| Street address |
Guyot Hall
|
| City |
Princeton |
| State/province |
NJ |
| ZIP/Postal code |
08540 |
| Country |
USA |
| |
|
| Platform ID |
GPL7261 |
| Series (1) |
| GSE12742 |
Phytoplankton community composition and gene expression involved in carbon and nitrogen assimilation |
|
