PC3 vs LNCaP amplified and unamplified miRNA
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE4572 | GEO | 2006/04/05
SECONDARY ACCESSION(S): PRJNA94407
REPOSITORIES: GEO
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2012-03-08 | GSE17317 | GEO
Project description:Siomycin A treatment in prostate cancer cell lines resulted in a concurrent inhibition of specific cell cycle genes and strongly impaired cell viability. Illumina microarray experiments were done using PC3 and LNCaP cell lines treated with 0.5 microM Siomaycin A either 24h or 48h in triplicates.
2012-10-19 | E-GEOD-36531 | biostudies-arrayexpress
Project description:Purpose: To examine the effects of proL1 upregulation on global gene expression in PC3 cells using RNA sequencing (RNA-Seq) Methods: PC3 cells were transformed to overexpress proL1 using lentiviral vectors. The proL1 overexpressing variant (PC3 proL1+) and their parental cell line were plated in 6-well plates in triplicate (3 wells for each cell line). After 3 days, their RNA was isolated using the Qiagen RNeasy Mini kit and their global gene expression patterns were analyzed using RNA-Seq Results: We identified 1698 differentially expressed genes between PC3 proL1+ and its parental cell line. Of these differentially expressed genes (DEGs), 209 were in common with LNCaP when proL1 was overexpressed. To identify biological functions that may be regulated through overexpression of proL1 in LNCaP cells, the list of DEGs was submitted to the DAVID, GOC, and KEGG databases, which identified 1250, 1366, and 480 unique genes within each database, respectively, which were then used for ontological analysis. According to these databases, proL1 overexpression regulated gene expression in ontological groups involved "anatomical structure development/morphogenesis" (more specifically "prostate gland morphogenesis"), extracellular matrix organization," "signaling," and "signal transduction. DEGs were also overrepresented in ontological groups potentially involved in vascularization and blood flow regulation. Analysis of the list of DEGs using the KEGG database identified the ontologic group "pathways in cancer" as having the greatest number of DEGs. DEGs were also identified with significant overrepresentation in specific biochemical pathways, such as the P13K-Akt, VEGF, and MAPK signaling pathways as well as steroid metabolic pathways. However, there were differences in the regulation of specific genes related to the androgen response between LNCaP and PC3. Unlike PC3, where overexpression of ProL1 caused a significant increase in expression of the androgen receptor gene (AR) and a decrease in expression of the estrogen receptor (ESR1), in LNCaP neither of these genes were changed in expression. In contrast, proL1 overexpression in LNCaP reduced expression of the progesterone receptor gene (PGR) but not in PC3 cells. Conclusion: Global analysis of the changes in gene expression caused by proL1 overexpression in PC3 and LNCaP cells supports that it has a role both in the modulation of genetic pathways involved in both overcoming hypoxia and the development of androgen-insensitivity. Opiorphins have previously been shown to be directly involved in regulation of blood-flow to tissues through their modulation of smooth muscle tone, and therefore their upregulation in tumors may directly contribute to overcoming the hypoxic barrier that develops in the growing tumor. In addition, overexpression of ProL1 in both PC3 and LNCaP cells modulated expression of genes involved in angiogenesis and morphogensis; the activation of these pathways would likely be involved in vascularization of the tumor and thereby also contribute to overcoming hypoxia. Overexpression of proL1 also affected genes involved in steroid metabolism and response pathways in both LNCaP and PC3, which could potentially contribute to the modulation of androgen sensitivity. In PC3 proL1+ cells we observed a significant upregulation of the Androgen Receptor (AR). Increased activity of the AR could subsequently lead to the activation of secondary messengers involved in modulating the activity of other signaling pathways such as the PI3K-Akt signaling and MAPK pathways, which had significant over-representation of DEGs in PC3 proL1+ cells. The PI3K-Akt signaling pathway is considered one of the most commonly dysregulated pathways in prostate cancer with approximately 40% of early stage, and 70-100% of advanced staged cancer exhibiting dysregulation of this pathway.
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Project description:Abstract: BACKGROUND: T7 based linear amplification of RNA is used to obtain sufficient antisense RNA for microarray expression profiling. We optimized and systematically evaluated the fidelity and reproducibility of different amplification protocols using total RNA obtained from primary human breast carcinomas and high-density cDNA microarrays. RESULTS: Using an optimized protocol, the average correlation coefficient of gene expression of 11,123 cDNA clones between amplified and unamplified samples is 0.82 (0.85 when a virtual array was created using repeatedly amplified samples to minimize experimental variation). Less than 4% of genes show changes in expression level by 2-fold or greater after amplification compared to unamplified samples. Most changes due to amplification are not systematic both within one tumor sample and between different tumors. Amplification appears to dampen the variation of gene expression for some genes when compared to unamplified poly(A)+ RNA. The reproducibility between repeatedly amplified samples is 0.97 when performed on the same day, but drops to 0.90 when performed weeks apart. The fidelity and reproducibility of amplification is not affected by decreasing the amount of input total RNA in the 0.3-3 micrograms range. Adding template-switching primer, DNA ligase, or column purification of double-stranded cDNA does not improve the fidelity of amplification. The correlation coefficient between amplified and unamplified samples is higher when total RNA is used as template for both experimental and reference RNA amplification. CONCLUSION: T7 based linear amplification reproducibly generates amplified RNA that closely approximates original sample for gene expression profiling using cDNA microarrays. This SuperSeries is composed of the SubSeries listed below.
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Project description:The study described a comprehensive high-fidelity method to successfully amplify low starting amounts of RNA extracted from FFPE tissue obtained from bronchial biopsies. Both amplified and unamplified RNA resulted in comparable gene expression for lung cancer and asthma samples.
2023-03-30 | GSE228217 | GEO
Project description:This SuperSeries is composed of the following subset Series: GSE3557: Effect of the amount of input total RNA on T7 amplification GSE3558: Effect of in vitro transcription time on the fidelity of T7-based RNA linear amplification GSE3559: Variation in cDNA microarray analysis of gene expression using unamplified poly(A)+ RNA GSE3560: Effects of template switching (TS) primer and cDNA cleanup columns on T7 based RNA linear amplification GSE3561: Effect of ligase on T7 based RNA linear amplification GSE3562: Effect of column cleanup on T7 based RNA linear amplification GSE3563: Correlation between expression levels of different tumors measured by poly(A)+RNA and aRNA Abstract: BACKGROUND: T7 based linear amplification of RNA is used to obtain sufficient antisense RNA for microarray expression profiling. We optimized and systematically evaluated the fidelity and reproducibility of different amplification protocols using total RNA obtained from primary human breast carcinomas and high-density cDNA microarrays. RESULTS: Using an optimized protocol, the average correlation coefficient of gene expression of 11,123 cDNA clones between amplified and unamplified samples is 0.82 (0.85 when a virtual array was created using repeatedly amplified samples to minimize experimental variation). Less than 4% of genes show changes in expression level by 2-fold or greater after amplification compared to unamplified samples. Most changes due to amplification are not systematic both within one tumor sample and between different tumors. Amplification appears to dampen the variation of gene expression for some genes when compared to unamplified poly(A)+ RNA. The reproducibility between repeatedly amplified samples is 0.97 when performed on the same day, but drops to 0.90 when performed weeks apart. The fidelity and reproducibility of amplification is not affected by decreasing the amount of input total RNA in the 0.3-3 micrograms range. Adding template-switching primer, DNA ligase, or column purification of double-stranded cDNA does not improve the fidelity of amplification. The correlation coefficient between amplified and unamplified samples is higher when total RNA is used as template for both experimental and reference RNA amplification. CONCLUSION: T7 based linear amplification reproducibly generates amplified RNA that closely approximates original sample for gene expression profiling using cDNA microarrays. Refer to individual Series
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