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Sample GSM319911 Query DataSets for GSM319911
Status Public on Sep 12, 2008
Title 400 ng rbcL from ST-30A
Sample type mixed
 
Channel 1
Source name particulate material from ~4 L of surface seawater
Organism uncultured organism
Characteristics 400 ng of rbcL PCR product prepared from cDNA extracted from sample ST-30A
phytoplankton
Sample collected April 2004
Treatment protocol Water was filtered onto 0.2 µm sterivex filters and immediately frozen at -80oC until extraction
Extracted molecule total RNA
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

Data table header descriptions
ID_REF
VALUE normalized fluorescence ratio of Cy3 (target)/Cy5(standard)

Data table
ID_REF VALUE
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20

Total number of rows: 47

Table truncated, full table size <1 Kbytes.




Supplementary file Size Download File type/resource
GSM319911.xls.gz 2.1 Mb (ftp)(http) XLS
Processed data included within Sample table

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