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| Status |
Public on Mar 01, 2012 |
| Title |
Identification of Oncogenic Potential of SIRT7 and Its Regulatory MicroRNAs in Liver Tumorigenesis |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
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| Summary |
To investigate the specific roles of SIRT7 in the development of HCC, we employed large-scale gene expression analysis to identify the molecular signature that may affect enabling characteristics of cancer cells. Differentially expressed genes were analyzed on the Hep3B cells transfected with SIRT7 shRNAs, and recapitulated molecular signatures that related to hallmarks of cancer.
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| Overall design |
For each of the experimental conditions, total RNA was extracted from three independent sets of the corresponding cell lines using TRIzol Reagent (Invitrogen), followed by clean up on Ambion columns (Illumina Total-Prep RNA Amplification Kit, Ambion). For each experimental condition, an RNA pool was then obtained by mixing equal quantities of total RNA from each of the three independent RNA extractions. Biotin-labelled cRNA targets were synthesized starting from 1.5 µg of total RNA. Double stranded cDNA synthesis was performed with Illumina® TotalPrep RNA Amplification Kit (Ambion), and biotin-UTP-labelled antisense RNA was transcribed in vitro using Ambion’s Kit. All steps of the labelling protocol were performed as suggested by Ambion (http://www.ambion.com/techlib/prot/ fm_IL1791.pdf). The size and the accuracy of quantitation of targets were checked by Experion (Bio-rad Laboratories., Hercules, CA) electrophoresis system, prior to and after cRNA purification. After purification, targets were diluted in hybridization buffer at a concentration of 240 ng/µl, and hybridization was allowed to proceed at 58°C for 20 h. For microarray analysis, the Illumina HumanHT-12 v4 Sentrix Expression BeadChip was used (Illumina, San Diego, CA). Hybridization of labelled cRNA to the BeadChip, washing, and scanning were performed according to the Illumina BeadStation 500× manual. The array signal was developed via 10-min incubation with streptavidin-Cy3. The HumanHT-12 v4 Sentrix Expression BeadChip was washed and subsequently dried via centrifugation for 4 min at a setting of 275 xg. The arrays were scanned on the Illumina BeadArray reader, a confocal-type imaging system with 532 (Cy3) nm laser illumination. Data from each sample was extracted with Genome Studio software (Illumina) using default parameters and then analyzed using GenPlex 3.0.
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| Contributor(s) |
Kim JK, Noh JH, Eun JW, Jung KH, Bae HJ, Xie HJ, Kim MG, Chang YG, Park WS, Lee JY, Nam SW |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| Submission date |
Oct 26, 2011 |
| Last update date |
Oct 18, 2022 |
| Contact name |
Jung Woo Eun |
| E-mail(s) |
jetaimebin@catholic.ac.kr
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| Organization name |
Ajou University of Korea
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| Street address |
Department of Gastroenterology
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| City |
Suwon, Korea |
| State/province |
Korea |
| ZIP/Postal code |
16499 |
| Country |
South Korea |
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| Platforms (1) |
| GPL10558 |
Illumina HumanHT-12 V4.0 expression beadchip |
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| Samples (2) |
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| Relations |
| BioProject |
PRJNA149423 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE33234_RAW.tar |
26.2 Mb |
(http)(custom) |
TAR |
| GSE33234_non-normalized.txt.gz |
792.1 Kb |
(ftp)(http) |
TXT |
| Processed data included within Sample table |
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