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SRP027258
Homo sapiens
36 Downloadable Samples
Illumina HiSeq 2000
Description
Epidemiological studies provide strong evidence that consumption of cruciferous vegetables, such as broccoli, can significantly reduce the risk of developing cancers. Sulforaphane (SFN), a phytochemical derived from cruciferous vegetables, induces anti-proliferative and pro-apoptotic responses in prostate cancer cells, but not in normal prostate cells. The mechanisms responsible for these specific chemopreventive properties remain unclear. We utilized RNA sequencing to test the hypothesis that SFN modifies the expression of genes that are critical in prostate cancer progression. Normal prostate epithelial cells, and androgen-dependent and androgen-independent prostate cancer cells were treated with 15 µM SFN and the transcriptome was determined at 6 and 24 hour time points. SFN altered the expression of ~3,000 genes in each cell line and the response was highly dynamic over time. SFN influenced the expression of genes in functional groups and pathways that are critical in cancer including cell cycle, apoptosis and angiogenesis, but the specific effects of SFN differed depending on the state of cancer progression. Network analysis suggested that a transcription factor that is overexpressed in many cancers, Specificity protein 1 (Sp1), is a major mediator of SFN-induced changes in gene expression. Nuclear Sp1 protein was significantly decreased by 24 hour SFN treatment in prostate cancer cells, while a related transcription factor, Sp3 protein was only modestly decreased in androgen-independent prostate cancer cells. Overall, the data show that SFN significantly affects gene expression in normal and cancer cells, with key targets in chemopreventive processes, making it a promising dietary anti-cancer agent. Overall design: Examination of how the transcriptome of normal and prostate cancer cells is altered by treatment with sulforaphane
Publication Title
Transcriptome analysis reveals a dynamic and differential transcriptional response to sulforaphane in normal and prostate cancer cells and suggests a role for Sp1 in chemoprevention.
Sample Metadata Fields
Specimen part, Subject, Time
View Samples- Homo sapiens
- 6 Downloadable Samples
Affymetrix Human Genome U133A Array (hgu133a)
Description
The purpose of this study was to search for microgravity-sensitive genes, specifically for apoptotic genes influenced by the microgravity environment and other genes related to immune response.
Publication Title
Gene expression alterations in activated human T-cells induced by modeled microgravity.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 6 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
The below table includes a smaller list of data that was analyzed by dChip and filtered by pvalue such that a file with about 4600 genes was obtained, which allowed for ease of use from 40,000 genes.
Publication Title
Identification of mechanosensitive genes in osteoblasts by comparative microarray studies using the rotating wall vessel and the random positioning machine.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 37 Downloadable Samples
- Illumina HiSeq 2000
Description
Purpose: Due to its high metastatic proclivity, pancreatic ductal adenocarcinoma (PDAC) is one of the most deadly types of cancer. Therefore, it is imperative to better understand how the disease spreads as it progresses. Using a novel genetically engineered mouse model that allows us to isolate a subpopulation of cancer cells with superior metastatic capacity, we show that this aggressive phenotype correlates exclusively with a strong hypoxia signature. We subsequently identified the novel hypoxia-inducible gene Blimp1, which appears to play a critical role in regulating the hypoxic response upon its induction. Furthermore, genetic ablation of Blimp1 greatly reduces the level of metastasis in a PDAC mouse model. The nature of this Blimp1-regulated hypoxia signature is very unstable, since the seeded metastatic lesions mostly re-adopt similar transcriptomic profiles as the primary tumors. In conclusion, our results offer a potential mechanistic insight into how hypoxia drives metastasis in PDAC. Methods: Pure, paired GFP-negative/Tomato-positive and GFP-positive/Tomato-positive cancer cells or pure Tomato-positive cancer cells were sorted from primary PDAC samples from 6 KPC-colors mice or KPCT mice, respectively, with the following criteria: single cell based on FSC-A/H; CD45-negative; CD31-negative; Ter119-negative; F4/80-negative; DAPI-negative; and Tomato-positive. RNA were extracted from 10^4 to 5x10^4 freshly sorted cancer cells using AllPrep DNA/RNA Micro Kit (Qiagen). RNA quality was assessed with the RNA6000 PicoAssay kit by using the Bioanalyzer 2100 (Agilent). All ex vivo RNA samples used for RNA-seq analyses had an RIN > 8.0. Total RNA (15 ng/sample) was used for cDNA synthesis and amplification with the Ovation RNA-Seq system (NuGEN Technologies, Inc.). Subsequently, the amplified DNA samples were fragmented through sonication (Covaris model S1) and subjected to library preparation using the Illumina TruSeqTM DNA sample preparation kit (Low-Throughput protocol) according to manufacturer''s protocol. The quality of purified cDNA library products was confirmed by bioanalyzer and prepared for cluster generation on HiSeq paired-end flow cells using the CBot automated cluster generation system followed by sequencing on HiSeq 2000 machines. We obtained 101bp, paired-end reads from fragments of an average length of 250bp. Subsequently, RNA-Seq reads were aligned to the mouse genome (mm10) using the STAR aligner with standard input parameters (Dobin et al., 2013). The number of reads uniquely aligned to exons of individual genes were counted with HTSeq against the UCSC KnownGene (mm10) transcriptome (Anders et al., 2015). Results: Compared to the GFP-negative counterparts, GFP-positive pure PDAC cancer cells express higher levels of genes that are highly enriched with hypoxia signature. Additionally, compared to the GFP-negative counterparts, GFP-positive pure PDAC cancer cells express lower levels of cell cycle-related genes. In contrast, pure cancer cells isolated based on locations reveal few consistent differentially expressed genes between primary tumor and liver metastases; no consistent differentially expressed gene between primary tumor and lymph node metastases. Conclusions: Transcriptome profiles of both GFP-negative/positive PDAC cancer cells suggest that Hmga2/GFP-expressing cancer cells are highly enriched for signatures that correspond to cells residing within hypoxic enrivonment. Overall design: Freshly sorted GFP/Hmga2-positive and GFP/Hmga2-negative PDAC cancer cells derived from tumors of 6 KPCT;Hmga2-CK/+ (KPC-colors) mice were subjected to transcriptome profiling by paired-end RNA-Seq (total of 6 pairs of samples with overall 12 samples). Additionally, pure Tomato-positive PDAC cancer cells isolated from different anatomical locations were also subjected to transcriptome profiling by paired-end RNA-Seq (n = 23, not including technical replicates).
Publication Title
BLIMP1 Induces Transient Metastatic Heterogeneity in Pancreatic Cancer.
Sample Metadata Fields
Specimen part, Subject
View Samples- Homo sapiens
- 10 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Resistance to CDK2 inhibitors is associated with selection of polyploid cells in CCNE1-amplified ovarian cancer.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 10 Downloadable Samples
Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
Cyclin E1 (CCNE1) is amplified in various tumor types including high-grade serous ovarian cancer where it is associated with poor clinical outcome. We have demonstrate that suppression of the Cyclin E1 partner kinase, CDK2, induces apoptosis in a CCNE1 amplicon-dependent manner. Little is known of mechanisms of resistance to CDK inhibitors. We therefore generated OVCAR-3 sublines with reduced sensitivity to CDK2 inhibitors and profiled by gene expression microarrays.
Publication Title
Resistance to CDK2 inhibitors is associated with selection of polyploid cells in CCNE1-amplified ovarian cancer.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 8 Downloadable Samples
- Illumina Genome Analyzer II
Description
The miR-16 family, which targets genes important for the G1-S transition, is a known modulator of the cell cycle, and members of this family are often deleted or down-regulated in many types of cancers. Here we report the reciprocal relationship - that of the cell cycle controlling the miR-16 family. Levels of this family increase rapidly as cells are arrested in G0. Conversely, as cells are released from G0 arrest, levels of the miR-16 family rapidly decrease. Such rapid changes are made possible by the unusual instabilities of several family members. The repression mediated by the miR-16 family is sensitive to these cell cycle changes, which suggests that the rapid up-regulation of the miR-16 family reinforces cell cycle arrest in G0. Upon cell cycle re-entry, the rapid decay of several members allows levels of the family to decrease, alleviating repression of target genes and allowing proper resumption of the cell cycle. Overall design: Small RNAs were profiled by high-throughput sequencing either during synchronous release after serum starvation or during cell-cycle arrest by contact inhibition.
Publication Title
MicroRNA destabilization enables dynamic regulation of the miR-16 family in response to cell-cycle changes.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Homo sapiens
- 7 Downloadable Samples
- Illumina HiSeq 2500
Description
Translation and mRNA decay are intimately connected processes, and translational inhibition often precedes and stimulates transcript degradation. Here, we have focused on methods that allow determination of mRNA stability on a transcriptome-wide scale. We describe experimental and computational methods for the two most commonly used approaches (transcriptional inhibition and metabolic labeling), and we discuss associated caveats. Overall design: Metabolic labeling time courses (1, 2, 4, 8, 12, 24 hr) using 4SU were performed in HEK293.
Publication Title
Determining mRNA half-lives on a transcriptome-wide scale.
Sample Metadata Fields
Treatment, Subject
View Samples- Danio rerio
- 12 Downloadable Samples
- IlluminaHiSeq2000
Description
Olfactory sensory neurons express just one out of a possible ~1000 odorant receptor genes, reflecting an exquisite mode of gene regulation. In one model, once an odorant receptor is chosen for expression, other receptor genes are suppressed by a negative feedback mechanism, ensuring a stable functional identity of the sensory neuron for the lifetime of the cell. The signal transduction mechanism subserving odorant receptor gene silencing remains obscure, however. Here we demonstrate in the zebrafish that odorant receptor gene silencing is dependent on receptor activity. Moreover, we show that signaling through G protein ß? subunits is both necessary and sufficient to suppress the expression of odorant receptor genes, and likely acts through histone methylation to maintain the silenced odorant receptor genes in transcriptionally inactive heterochromatin. These results provide new insights linking receptor activity with the epigenetic mechanisms responsible for ensuring the expression of one odorant receptor per olfactory sensory neuron. Overall design: Total 6 samples were analyzed-3 controls & 3 samples
Publication Title
Normalization of RNA-seq data using factor analysis of control genes or samples.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 4 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Abstract. The role of platelets in hemostasis and thrombosis is clearly established; however, the mechanisms by which platelets mediate inflammatory and immune pathways are less well understood. Platelets interact and modulate the function of blood and vascular cells by releasing bioactive molecules. Although the platelet is anucleate, it contains transcripts that may mirror disease. Platelet mRNA is only associated with low-level protein translation, however, platelets have a unique membrane structure allowing for the passage of small molecules, leading to the possibility that its cytoplasmic RNA may be passed to nucleated cells. To examine this question, platelet-like particles with labeled RNA were co-cultured with vascular cells. Co-culture of platelet-like particles with activated THP-1, monocytic, and endothelial cells led to visual and functional RNA transfer. Post-transfer microarray gene expression analysis of THP-1 cells showed an increase in HBG1/HBG2 and HBA1/HBA2 expression which was directly related to the transfer. Infusion of wild-type platelets into a TLR2 deficient mouse model established in vivo confirmation of select platelet RNA transfer to leukocytes. By specifically transferring green fluorescent protein, it was also observed that external RNA was functional in the recipient cells. The observation that platelets possess the capacity to transfer cytosolic RNA suggests a new function for platelets in the regulation of vascular homeostasis.
Publication Title
Platelets and platelet-like particles mediate intercellular RNA transfer.
Sample Metadata Fields
Specimen part, Cell line
View Samples