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Status |
Public on May 22, 2012 |
Title |
Influence of RNA Labeling on Expression Profiling of MicroRNAs |
Platform organism |
synthetic construct |
Sample organisms |
Homo sapiens; synthetic construct |
Experiment type |
Non-coding RNA profiling by array
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Summary |
Several technical parameters are now being optimized for microRNA expression profiling experiments, but the finite amount of total RNA available continues to bottleneck clinical investigations. We used microarrays to determine the influence of the labeling reagent on total RNA requirements and data quality.
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Overall design |
Human brain/lung samples were each labeled in duplicate, at 1.0ug, 0.5ug, 0.2ug, and 0.1ug of total RNA, using two microRNA labeling kits (Genisphere Biotin and Biotin-HSR) that utilize the same labeling procedure but differ in the composition of the labeling reagent used to label the microRNA molecules in the samples. A total of 32 arrays were used for this experiment. Additionally, synthetic microRNA spike-in experiments were also performed to establish the signal dynamic range of the microarray using the Biotin-HSR labeling kit. Two-fold serial dilution samples were prepared that contained from 5000 to 4.88 attomoles of miRNA. A total of 12 arrays were used for this experiment, including a negative control sample.
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Contributor(s) |
Kaddis JS, Wai DH, Bowers J, Hartmann N, Baeriswyl L, Bajaj S, Anderson MJ, Getts RC, Triche TJ |
Citation(s) |
22074760 |
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Submission date |
Jun 16, 2011 |
Last update date |
May 02, 2017 |
Contact name |
John S. Kaddis |
E-mail(s) |
jkaddis@coh.org
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Organization name |
City of Hope
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Department |
Diabetes and Cancer Discovery Science
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Street address |
1500 East Duarte Road
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City |
Duarte |
State/province |
CA |
ZIP/Postal code |
91010-3000 |
Country |
USA |
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Platforms (1) |
GPL8786 |
[miRNA-1] Affymetrix Multispecies miRNA-1 Array |
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Samples (44)
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GSM743799 |
Biotin-HSR labeled brain samples, 100ng total RNA, technical rep1 |
GSM743800 |
Biotin-HSR labeled brain samples, 100ng total RNA, technical rep2 |
GSM743801 |
Biotin-HSR labeled brain samples, 200ng total RNA, technical rep1 |
GSM743802 |
Biotin-HSR labeled brain samples, 200ng total RNA, technical rep2 |
GSM743803 |
Biotin-HSR labeled brain samples, 500ng total RNA, technical rep1 |
GSM743804 |
Biotin-HSR labeled brain samples, 500ng total RNA, technical rep2 |
GSM743805 |
Biotin-HSR labeled brain samples, 1000ng total RNA, technical rep1 |
GSM743806 |
Biotin-HSR labeled brain samples, 1000ng total RNA, technical rep2 |
GSM743807 |
Biotin-HSR labeled lung samples, 100ng total RNA, technical rep1 |
GSM743808 |
Biotin-HSR labeled lung samples, 100ng total RNA, technical rep2 |
GSM743809 |
Biotin-HSR labeled lung samples, 200ng total RNA, technical rep1 |
GSM743810 |
Biotin-HSR labeled lung samples, 200ng total RNA, technical rep2 |
GSM743811 |
Biotin-HSR labeled lung samples, 500ng total RNA, technical rep1 |
GSM743812 |
Biotin-HSR labeled lung samples, 500ng total RNA, technical rep2 |
GSM743813 |
Biotin-HSR labeled lung samples, 1000ng total RNA, technical rep1 |
GSM743814 |
Biotin-HSR labeled lung samples, 1000ng total RNA, technical rep2 |
GSM743815 |
Biotin-Only labeled brain samples, 100ng total RNA, technical rep1 |
GSM743816 |
Biotin-Only labeled brain samples, 100ng total RNA, technical rep2 |
GSM743817 |
Biotin-Only labeled brain samples, 200ng total RNA, technical rep1 |
GSM743818 |
Biotin-Only labeled brain samples, 200ng total RNA, technical rep2 |
GSM743819 |
Biotin-Only labeled brain samples, 500ng total RNA, technical rep1 |
GSM743820 |
Biotin-Only labeled brain samples, 500ng total RNA, technical rep2 |
GSM743821 |
Biotin-Only labeled brain samples, 1000ng total RNA, technical rep1 |
GSM743822 |
Biotin-Only labeled brain samples, 1000ng total RNA, technical rep2 |
GSM743823 |
Biotin-Only labeled lung samples, 100ng total RNA, technical rep1 |
GSM743824 |
Biotin-Only labeled lung samples, 100ng total RNA, technical rep2 |
GSM743825 |
Biotin-Only labeled lung samples, 200ng total RNA, technical rep1 |
GSM743826 |
Biotin-Only labeled lung samples, 200ng total RNA, technical rep2 |
GSM743827 |
Biotin-Only labeled lung samples, 500ng total RNA, technical rep1 |
GSM743828 |
Biotin-Only labeled lung samples, 500ng total RNA, technical rep2 |
GSM743829 |
Biotin-Only labeled lung samples, 1000ng total RNA, technical rep1 |
GSM743830 |
Biotin-Only labeled lung samples, 1000ng total RNA, technical rep2 |
GSM743831 |
Biotin-HSR labeled synthetic miRNA spike in, 0 attomoles |
GSM743832 |
Biotin-HSR labeled synthetic miRNA spike in, 4.88 attomoles |
GSM743833 |
Biotin-HSR labeled synthetic miRNA spike in, 9.77 attomoles |
GSM743834 |
Biotin-HSR labeled synthetic miRNA spike in, 19.53 attomoles |
GSM743835 |
Biotin-HSR labeled synthetic miRNA spike in, 39.06 attomoles |
GSM743836 |
Biotin-HSR labeled synthetic miRNA spike in, 78.13 attomoles |
GSM743837 |
Biotin-HSR labeled synthetic miRNA spike in, 156.25 attomoles |
GSM743838 |
Biotin-HSR labeled synthetic miRNA spike in, 312.5 attomoles |
GSM743839 |
Biotin-HSR labeled synthetic miRNA spike in, 625 attomoles |
GSM743840 |
Biotin-HSR labeled synthetic miRNA spike in, 1250 attomoles |
GSM743841 |
Biotin-HSR labeled synthetic miRNA spike in, 2500 attomoles |
GSM743842 |
Biotin-HSR labeled synthetic miRNA spike in, 5000 attomoles |
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Relations |
BioProject |
PRJNA144079 |
Supplementary file |
Size |
Download |
File type/resource |
GSE30045_RAW.tar |
7.3 Mb |
(http)(custom) |
TAR (of CEL) |
Processed data included within Sample table |
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