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| Status |
Public on Apr 15, 2010 |
| Title |
Preferred analysis methods for Affymetrix GeneChips. II. An expanded, balanced, wholly-defined spike-in dataset |
| Organism |
Drosophila melanogaster |
| Experiment type |
Other
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| Summary |
We present a new wholly defined Affymetrix spike-in dataset consisting of 18 microarrays. Over 5700 RNAs are spiked in at relative concentrations ranging from 1- to 4-fold, and the arrays from each condition are balanced with respect to both total RNA amount and degree of positive- versus negative-fold change. We use this new “Platinum Spike” dataset to evaluate microarray analysis routes and contrast the results to those achieved using our earlier Golden Spike dataset.
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| Overall design |
PCR products from 5725 Drosophila Gene Collection release 1.0 (DGCr1) cDNA clones were collected into 28 distinct pools, and three independent in vitro transcription and labeling reactions were performed for each pool. Labeled cRNAs from each individual pool were then added at specified amounts to samples A and B to achieve the desired fold change differences between samples. 24 cRNAs generated from DGCr2 cDNA clones were added to each sample in known concentrations before hybridization.
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| Web link |
http://www2.ccr.buffalo.edu/halfon/platinum_spike/platinumspikedownloads.html
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| Contributor(s) |
Halfon MS, Zhu Q |
| Citation(s) |
20507584 |
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| Submission date |
Apr 14, 2010 |
| Last update date |
Aug 28, 2018 |
| Contact name |
Qianqian Zhu |
| Organization name |
State University of New York at Buffalo
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| Department |
Biochemistry
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| Lab |
Marc S. Halfon
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| Street address |
701 Ellicott St.
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| City |
Buffalo |
| State/province |
NY |
| ZIP/Postal code |
14203 |
| Country |
USA |
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| Platforms (1) |
| GPL1322 |
[Drosophila_2] Affymetrix Drosophila Genome 2.0 Array |
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| Samples (18)
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| GSM533369 |
condition A, independent labeling 1, technical replicate alpha |
| GSM533370 |
condition A, independent labeling 1, technical replicate beta |
| GSM533371 |
condition A, independent labeling 1, technical replicate gamma |
| GSM533372 |
condition A, independent labeling 2, technical replicate alpha |
| GSM533373 |
condition A, independent labeling 2, technical replicate beta |
| GSM533374 |
condition A, independent labeling 2, technical replicate gamma |
| GSM533375 |
condition A, independent labeling 3, technical replicate alpha |
| GSM533376 |
condition A, independent labeling 3, technical replicate beta |
| GSM533377 |
condition A, independent labeling 3, technical replicate gamma |
| GSM533378 |
condition B, independent labeling 1, technical replicate alpha |
| GSM533379 |
condition B, independent labeling 1, technical replicate beta |
| GSM533380 |
condition B, independent labeling 1, technical replicate gamma |
| GSM533381 |
condition B, independent labeling 2, technical replicate alpha |
| GSM533382 |
condition B, independent labeling 2, technical replicate beta |
| GSM533383 |
condition B, independent labeling 2, technical replicate gamma |
| GSM533384 |
condition B, independent labeling 3, technical replicate alpha |
| GSM533385 |
condition B, independent labeling 3, technical replicate beta |
| GSM533386 |
condition B, independent labeling 3, technical replicate gamma |
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| Relations |
| BioProject |
PRJNA126141 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE21344_RAW.tar |
35.6 Mb |
(http)(custom) |
TAR (of CEL) |
| GSE21344_allclones_fcvalue.txt.gz |
17.5 Kb |
(ftp)(http) |
TXT |
| Processed data not applicable for this record |
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