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GEO help: Mouse over screen elements for information. |
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| Status |
Public on May 10, 2014 |
| Title |
Global assessment of Antrodia cinnamomea induced microRNA and mRNA transcriptomic alterations in hepatocarcinoma cells |
| Organisms |
Homo sapiens; Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
Non-coding RNA profiling by high throughput sequencing
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| Summary |
Antrodia cinnamomea (Ac), a traditional medicine and an endemic fungus in Taiwan, has been used in cancer research. Recent research has revealed decreased cell proliferation after treatment of Ac on tumor. In this study, we profiled the 2 hours and 4 hours genome-wide miRNA and mRNA transcriptome by next-generation sequencing techniques to report the early apoptotic effect on Ac fruiting body extract treated human hepatocarcinoma cells, SK-HEP-1, instead of prolonged treatment. Results showed that miRNAs were globally downregulated during the first 2-4 hours in, and solely in, AcFBE-treated SK cells. The inhibition of miRNAs imposed no discrimination against any particular miRNA species, but oncogenic miR-21, miR-191 and two oncogenic clusters miR-17-92 and miR-106b-25 were among the most significantly inhibited miRNAs. In addition to miRNA expression, mRNA transcriptome data indicated the association of apoptosis mechanism with AcFBE treatment. Western blotting indicated a decrease in key proteins Drosha and Dicer required for miRNA biogenesis, and an increase of XRN2 involved in miRNA degradation. Our results suggest that miRNAs appeared to be the prime targets of Ac in disrupting multiple miRNA regulatory pathways and global disruption of miRNA transcriptome resulting in activation of extrinsic and intrinsic (mitochondrial) pathways.
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| Overall design |
Human liver SK-Hep-1 cells with or without Antrodia cinnamomea treatment at 2 hours and 4 hours were sequenced by SOLiD 3 and SOLiD 5500xl to obtain miRNA profiles; mRNA profiles also were profiled by SOLID 3. Mouse liver BNL CL.2 cells with or without Antrodia cinnamomea treatment at 2 hours and 4 hours were sequenced by SOLiD 3 to obtain miRNA profiles.
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| Contributor(s) |
Lu Y, Thang WC |
| Citation(s) |
24358224 |
| Submission date |
Jun 26, 2013 |
| Last update date |
Aug 22, 2019 |
| Contact name |
mike thang |
| Organization name |
Academia Sinica
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| Department |
Genome Research Center
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| Lab |
2L11
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| Street address |
128 Academia Road, Section 2, Nankang
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| City |
Taipei |
| State/province |
Taipei |
| ZIP/Postal code |
115 |
| Country |
Taiwan |
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| Platforms (3) |
| GPL9442 |
AB SOLiD System 3.0 (Homo sapiens) |
| GPL15907 |
AB 5500xl Genetic Analyzer (Mus musculus) |
| GPL16288 |
AB 5500xl Genetic Analyzer (Homo sapiens) |
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| Samples (16)
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| GSM1174925 |
SK-HEP-1, 4T, mRNA (SOLID 3) |
| GSM1174926 |
SK-HEP-1, 2U, miRNA (SOLID 3) |
| GSM1174927 |
SK-HEP-1, 4U, miRNA (SOLID 3) |
| GSM1174928 |
SK-HEP-1, 2T, miRNA (SOLID 3) |
| GSM1174929 |
SK-HEP-1, 4T, miRNA (SOLID 3) |
| GSM1174930 |
SK-HEP-1, 2U, miRNA (SOLiD 5500xl) |
| GSM1174931 |
SK-HEP-1, 4U, miRNA (SOLiD 5500xl) |
| GSM1174932 |
SK-HEP-1, 2T, miRNA (SOLiD 5500xl) |
| GSM1174933 |
SK-HEP-1, 4T, miRNA (SOLiD 5500xl) |
| GSM1174934 |
BNL CL.2, 2U, miRNA (SOLiD 5500xl) |
| GSM1174935 |
BNL CL.2, 4U, miRNA (SOLiD 5500xl) |
| GSM1174936 |
BNL CL.2, 2T, miRNA (SOLiD 5500xl) |
| GSM1174937 |
BNL CL.2, 4T, miRNA (SOLiD 5500xl) |
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| Relations |
| BioProject |
PRJNA209709 |
| SRA |
SRP026342 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE48327_Transcriptome.txt.gz |
223.9 Kb |
(ftp)(http) |
TXT |
| GSE48327_fCL_5500.txt.gz |
2.7 Kb |
(ftp)(http) |
TXT |
| GSE48327_miRNA_solid3.txt.gz |
3.0 Kb |
(ftp)(http) |
TXT |
| GSE48327_miRNA_solid5500.txt.gz |
2.6 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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