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GSE23388
Homo sapiens
4 Downloadable Samples
Illumina HumanHT-12 V3.0 expression beadchip
Description
Microarray-based DNA methylation and gene expression profiling was carried out using a panel of prostate cancer cell lines (LNCaP-FGC, DU-145, and PC-3) and the control normal prostate RWPE1 cell line. The identification of prostate cancer-specific methylation markers was based on the following criteria: a difference in DNA methylation level () of at least 0.5, and at least a 2-fold difference in expression level between cancer and control cells. Using highly stringent selection criteria, we identified novel hypermethylated genes whose expression was silenced in prostate cancer cells.
Publication Title
EFEMP1 as a novel DNA methylation marker for prostate cancer: array-based DNA methylation and expression profiling.
Sample Metadata Fields
Specimen part, Cell line
View Samples- Homo sapiens
- 43 Downloadable Samples
Illumina HiSeq 2000
Description
The objective of this study is to identify gene signature associated with castration-refractory prostate cancer (CRPC) development. We carried out RNA-seq based transcriptome profiling using 45 prostate samples with various disease progression steps such as benign prostate hyperplasia (BPH), primary cancer of prostate (CaP), advanced CaP and CRPC. Via various statistical analyses, we identified significant gene set associated with each progression step and observed that AR was the only gene feature associated with all progression steps, indicating that AR is the crucial mediator of and has a diverse activity across the CaP progressions. Among the samples in this data set, there are 4 pairs of advanced CaP and CRPC samples, in which each pair was obtained from the same patient. Using these paired samples, we also determined differentially expressed genes between advanced CaP and CRPC, and performed comparative analysis of significant gene lists in matched sample pairs and in unpaired remained samples. By assessing expression difference between advanced CaP and CRPC groups, 309 and 182 genes were statistically significant in paired and unpaired samples, respectively (P < 0.001). When these two gene lists were compared, a total of 15 genes were common and applied to a number of downstream experimental assays. Overall design: RNA-seq data of 45 CRPC samples were generated. Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer''s protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light. Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer's protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR. Sequencing was performed in paired end reads (2x100 bp) using Hiseq-2000 (Illumina).
Publication Title
Transcriptomic features of primary prostate cancer and their prognostic relevance to castration-resistant prostate cancer.
Sample Metadata Fields
Subject
View Samples- Sus scrofa
- 8 Downloadable Samples
- Affymetrix Porcine Genome Array (porcine)
Description
There are clear phenotypic differences between Korean native pig (KNP) and Yorkshire (YS) breeds because of different interests for selection. YS has been artificially selected by industrial interests such as a growth rate and a lean meat production, however, KNP has been maintained as a regional breed by local interests such as a fat content in or between muscle and a disease resistance. A comparison of gene expression profile from a major tissue liver can reflect the overall effects of the artificial selection between the two pig breeds through long history. KNP (n=4) and YS (n=4) pigs were raised under the identical conditions. Global gene expression levels were measured in liver samples from these pigs using Affymetrix porcine genome array containing 23,937 probe sets. The clustering analysis based on the individual transcriptome data showed a clear separation between two breeds in the liver tissue. We collected hepato-transcriptome data including 11,993 genes fully detected from four independent samples either in KNP or in YS. Based on both minimum positive false discovery rate (less than 15%) and fold change (|FC| > 1.5), 160 differentially expressed genes (DEGs) were collected from the liver between the two breeds. The functional analysis of these DEGs indicated clear distinctions in intra- and extra-cellular structure, cell proliferation, membrane trafficking, glycolytic pathway, mitochondrial function, protein metabolism, and immune response. The functional characteristics based on the DEGs were useful indicators to explain the differences between these two breeds developed for the specific purposes each other. The hepatic DGEs indicate that the YS has been lost expressivity of genes not required for the fast growth but maintained expressivity of genes for lean muscle production. The tissue-wise gene expression profiles indicate that the liver could be a major place to make the economic distinction between these two pig breeds.
Publication Title
Differences in hepatic gene expression as a major distinguishing factor between Korean native pig and Yorkshire.
Sample Metadata Fields
Age, Specimen part
View Samples- Homo sapiens
- 15 Downloadable Samples
- IlluminaHiSeq2000, IlluminaGenomeAnalyzerIIx
Description
To understand epigenetic changes in the distal regulatory as well as proximal regions, we performed RNA-seq, MBD-seq, and H3K27ac ChIP-seq on gastric tissues and cell lines. Overall design: mRNA sequencing profiles of normal tissue (n), purified gastric cancer (sc), and cultured gastric cancer cell (dc) were generated by deep sequencing, in five samples from three patients (csc1, csc2, csc3) and two replicates (csc1_sc2, csc1_sc3), using Illumina GAIIx and HiSeq2000.
Publication Title
Integrated epigenomic analyses of enhancer as well as promoter regions in gastric cancer.
Sample Metadata Fields
No sample metadata fields
View Samples- Sus scrofa
- 8 Downloadable Samples
- Affymetrix Porcine Genome Array (porcine)
Description
The pig could be a useful model to characterize molecular aspects determining several delicate phenotypes because they have been bred for those characteristics. The Korean native pig (KNP) is a regional breed in Korea that was characterized by relatively high intramuscular fat content and reddish meat color compared to other western breeds such as Yorkshire (YS). YS grew faster and contained more lean muscle than KNP. We compared the KNP to Yorksire to find molecular clues determining muscle characteristics. The comparison of skeletal gene expression profiles between these two breeds showed molecular differences in muscle. We found 82 differentially expressed genes (DEGs) defined by fold change (more than 1.5 fold difference) and statistical significance (within 5% of false discovery rate). Functional analyses of these DEGs indicated up-regulation of most genes involved in cell cycle arrest, down-regulation of most genes involved in cellular differentiation and its inhibition, down-regulation of most genes encoding component of muscular-structural system, and up-regulation of most genes involved in diverse metabolism in KNP. Especially, DEGs in above-mentioned categories included a large number of genes encoding proteins directly or indirectly involved in p53 pathway. Our results indicated a possible role of p53 to determine muscle characteristics between these two breeds.
Publication Title
Transcriptional alteration of p53 related processes as a key factor for skeletal muscle characteristics in Sus scrofa.
Sample Metadata Fields
Age, Specimen part
View Samples- Homo sapiens
- 8 Downloadable Samples
- Illumina HumanHT-12 V3.0 expression beadchip
Description
In order to investigate the role of reptin methylation on the expression of hypoxia-responsive genes across the whole genome, we performed a microarray analysis from RNAs isolated from MCF7 cells expressing either control shRNA (shRNA) or reptin shRNA (shreptin) in normoxic and hypoxic conditions.
Publication Title
Negative regulation of hypoxic responses via induced Reptin methylation.
Sample Metadata Fields
Specimen part, Cell line
View Samples- Homo sapiens
- 15 Downloadable Samples
- Illumina HiSeq 2500
Description
We established PDX lines from diffuse type gastric cancers (DGCs). Using these cells, we carried out RNA-seq based transcriptome profiling using 15 stomach samples including three PDX lines (HGC-3, HGC-8, and HGC-20) and normal-looking surrounding tissues. Via comparative analysis between cells and tissues, we identified significant gene set associated with each cell and observed that genes involved in AKT signalling pathway were commonly associated with all PDX lines. Overall design: RNA-seq data of 15 gastric samples were generated. Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light. Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer's protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR. Sequencing was performed in paired end reads (2x75 bp) using Hiseq-2500 (Illumina).
Publication Title
Identification of a molecular signature of prognostic subtypes in diffuse-type gastric cancer.
Sample Metadata Fields
Subject
View Samples- Mus musculus
- 1 Downloadable Sample
- Illumina MouseRef-8 v2.0 expression beadchip
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
LATS-YAP/TAZ controls lineage specification by regulating TGFβ signaling and Hnf4α expression during liver development.
Sample Metadata Fields
Sex, Specimen part
View Samples- Mus musculus
- 8 Downloadable Samples
- IlluminaHiSeq2000
Description
RNA-sequencing results with in vitro cultured control and Lats1/2 deficient hepatoblasts, in vitro differentiated control and Lats1/2 deficient hepatocytes and biliary epithelial cells Overall design: To investigate changes in gene expression by loss of Lats1 and Lats2 during hepatocyte or biliary epithelial cell differentiation, we performed multiplex RNA-sequecing with in vitro cultured hepatoblasts, in vitro differentiated hepatocytes and biliary epithelial cells
Publication Title
LATS-YAP/TAZ controls lineage specification by regulating TGFβ signaling and Hnf4α expression during liver development.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 1 Downloadable Sample
- Illumina MouseRef-8 v2.0 expression beadchip
Description
Lats1-/-;Lats2fl/fl;Alb-Cre pups and control pups were sacrificed at 1 day after birth
Publication Title
LATS-YAP/TAZ controls lineage specification by regulating TGFβ signaling and Hnf4α expression during liver development.
Sample Metadata Fields
Sex, Specimen part
View Samples