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| Status |
Public on Oct 14, 2011 |
| Title |
Gene expression profiles due to common seed sequence of members of miR-302/372/373/520 family miRNAs and dsEcad640 in human PC-3 cells |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
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| Summary |
To examine the genome-wide gene regulation due to the common seed sequence of the members of miR-302/3272/3273/520 family miRNAs and dsEcad640, we performed microarray profiling of gene expression by the transfection of chemically synthesized dsEcad640, miR-302a,miR-372, miR-373, miR-520c,and miR-520f duplexes into PC-3 cells.
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| Overall design |
Chemically synthesized dsEcad640, miR-302a, miR-372, miR-373, miR-520c,and miR-520f duplexes were transfected into PC-3 cells. At 24 hours after transfection,the total RNA was extracted using the RNeasy Mini Kit (Qiagen). As a control, mock transfected cells treated with transfection reagent without siRNA and miRNA were used.Transfection was carried out four times independently, and the RNA quality was examined using Bioanalyzer (Agilent). Mixed RNA samples (150 ng total) of four experiments were used for the microarray analysis. After cDNA was synthesized with the Agilent One Color Spike Mix Kit, cRNA was prepared using the Quick Amp Labeling Kit (Agilent), labeled with Cy-3, and purified with the RNeasy Mini Kit (Qiagen).The cRNA was hybridized against the Agilent Whole Human Genome Microarray (4 × 44 K multipack format) at 65°C for 17 hours, then washed with Gene Expression Wash Buffer 1 and Wash Buffer 2 (Agilent) in 0.005% Triton X-102. The microarray slide was scanned using the DNA Microarray Scanner (Agilent) and quantified using Feature Extraction Software (Agilent).
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| Contributor(s) |
Mazda M, Nishi K, Naito Y, Ui-Tei K |
| Citation(s) |
22205962 |
| Submission date |
Oct 14, 2011 |
| Last update date |
Jan 23, 2019 |
| Contact name |
Kumiko Ui-Tei |
| E-mail(s) |
ktei@bi.s.u-tokyo.ac.jp
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| Phone |
+81-03-5841-3044
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| Fax |
+81-03-5841-3044
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| URL |
http://ui-tei.rnai.jp/index.html
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| Organization name |
The University of Tokyo
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| Department |
Biophysics and Biochemistry, Graduate School of Science
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| Lab |
Ui-Tei laboratory
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| Street address |
2-11-16 Yayoi Bunkyo-ku
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| City |
Tokyo |
| ZIP/Postal code |
113-0032 |
| Country |
Japan |
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| Platforms (1) |
| GPL6480 |
Agilent-014850 Whole Human Genome Microarray 4x44K G4112F (Probe Name version) |
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| Samples (11)
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| GSM817601 |
PC-3 cell transfection with mock, sample 1 [Set 1] |
| GSM817602 |
PC-3 cell transfection with dsEcad-640, sample 2 [Set 1] |
| GSM817603 |
PC-3 cell transfection with miR-302a, sample 3 [Set 1] |
| GSM817605 |
PC-3 cell transfection with miR-372, sample 4 [Set 1] |
| GSM817758 |
PC-3 cell transfection with miR-530f, sample 6 [Set 2] |
| GSM817760 |
PC-3 cell transfection with miR-373, sample 7 [Set 2] |
| GSM817762 |
PC-3 cell transfection with mock, sample 8 [Set 2] |
| GSM817828 |
PC-3 cell transfection with mock, sample 9 [Set 3] |
| GSM817830 |
PC-3 cell transfection with miR-372, sample 10 [Set 3] |
| GSM817832 |
PC-3 cell transfection with mock, sample 11 [Set 3] |
| GSM817834 |
PC-3 cell transfection with miR-520c, sample 12 [Set 3] |
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| Relations |
| BioProject |
PRJNA146517 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE32999_RAW.tar |
85.5 Mb |
(http)(custom) |
TAR (of TXT) |
| Processed data included within Sample table |
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