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SRP136107
Mus musculus
9 Downloadable Samples
Illumina HiSeq 2500
Description
Purpose: The goal of this study is to evaluate the transcriptome profiling (RNA-seq) of dormant and proliferating breast cancer cells using an in vitro 3D model Methods: mRNA profiles of D2.0R cells growing either on basal membrane extracts (BME) (dormant phase) or BME + Collagen (COL) (proliferative phase) at days 1 or 5 of culture were generated by deep sequencing in triplicate with Ilumina HiSeq2500 using Illumina TruSeq V4. Aligned reads (BAM files) were analysed using PartekFlow software for differential expression and gene enrichment analysis. Comparisons used Partek Gene Specific Analysis (GSA) algorithm and multiple comparisons were corrected using False Discovery Rate (FDR), which was set at 0.05 Results: Using an optimized data analysis workflow, we mapped about 118 – 133 million reads per sample to the mouse genome (build mm9). Total alignment with reference genome is between 81-90%. RNA-seq identified 5,524 transcripts showing differential expression between the D2.0R cells cultured on BME + COL vs D2.0R cells cultured on BME matrices at day 5, with a fold change =1.5 or =-1.5 and p value <0.05. On the other hand, only 1,097 were found to be differentially expressed between D2.0R cells growing on BME matrices at day 5 and day 1, with a fold change =1.5 or =-1.5 and p value <0.05. Hierarchical clustering of differentially expressed genes uncovered several as yet uncharacterized genes that may contribute to breast cancer dormancy and identifies autophagy as a top biological process activated in dormant D2.0R cells. Conclusions: Our study represents a detailed analysis of the transcriptomes of dormant and proliferating D2.0R cells, with three biologic replicates, generated by RNA-seq technology. RNA-seq based transcriptome characterization identifies autophagy as the most prevalent upregulated pathway in dormant breast cancer cells. Overall design: mRNA profiles of D2.0R cells after culture on BME or BME + COL matrices for 1 or 5 days were generated by deep sequencing in triplicate with Ilumina HiSeq2500 using Illumina TruSeq V4.
Publication Title
Autophagy promotes the survival of dormant breast cancer cells and metastatic tumour recurrence.
Sample Metadata Fields
Specimen part, Subject
View Samples- Homo sapiens
- 60 Downloadable Samples
Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Transcriptional shift identifies a set of genes driving breast cancer chemoresistance.
Sample Metadata Fields
Sex, Age, Specimen part, Treatment
View Samples- Homo sapiens
- 28 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
The aim of this study was to compare the gene expression profile changes breast tumors after the treatment with Anthracyclines and Taxanes. To this end, an oligonucleotide microarray was performed (Affymetrixs HG-U133 Plus 2.0 array). This gene expression study was carried out on the biopsied tumor samples previous being treated with chemotherapy, and subsequently compared with themselves once treatment schedule ended. The post-chemotherapy biopsy was obtained from the surgical piece. The goal of this study was the finding of several genes related to apoptosis, proliferation, differentiation, survival and transformation-related genes and correlating their differences in expression with the degree of response to chemotherapy, determined by the Miller and Payne histological grading system.
Publication Title
Transcriptional shift identifies a set of genes driving breast cancer chemoresistance.
Sample Metadata Fields
Sex, Age, Specimen part, Treatment
View Samples- Homo sapiens
- 19 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
The aim of this study was to compare the gene expression profile changes breast tumors after the treatment with Anthracyclines and Taxanes. To this end, an oligonucleotide microarray was performed (Affymetrixs HG-U133 Plus 2.0 array). This gene expression study was carried out on the biopsied tumor samples previous being treated with chemotherapy, and subsequently compared with themselves once treatment schedule ended. The post-chemotherapy biopsy was obtained from the surgical piece. The goal of this study was the finding of several genes related to apoptosis, proliferation, differentiation, survival and transformation-related genes and correlating their differences in expression with the degree of response to chemotherapy, determined by the Miller and Payne histological grading system.
Publication Title
Transcriptional shift identifies a set of genes driving breast cancer chemoresistance.
Sample Metadata Fields
Sex, Age, Specimen part, Treatment
View Samples- Homo sapiens
- 13 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
The aim of this study was to compare the gene expression profile changes breast tumors after the treatment with Anthracyclines and Taxanes. To this end, an oligonucleotide microarray was performed (Affymetrixs HG-U133 Plus 2.0 array). This gene expression study was carried out on the biopsied tumor samples previous being treated with chemotherapy, and subsequently compared with themselves once treatment schedule ended. The post-chemotherapy biopsy was obtained from the surgical piece. The goal of this study was the finding of several genes related to apoptosis, proliferation, differentiation, survival and transformation-related genes and correlating their differences in expression with the degree of response to chemotherapy, determined by the Miller and Payne histological grading system.
Publication Title
Transcriptional shift identifies a set of genes driving breast cancer chemoresistance.
Sample Metadata Fields
Sex, Age, Specimen part, Treatment
View Samples- Rattus norvegicus
- 10 Downloadable Samples
- Affymetrix Rat Genome 230 2.0 Array (rat2302)
Description
The aim of this study was to compare the gene expression profile changes of DMBA-induced rat breast tumors after treatment with hydroxytyrosol (a natural compound from virgin olive oil). To this end, a cDNA microarray experiment was performed (Affymetrixs Rat Genome 230 2.0 array). This gene expression study was carried out on the tumor biopsy samples prior to hydroxytyrosol treatment, and compared with matched tumor biopsy samples after completion of the hydroxytyrosol treatment schedule. The result of this study was the identification of several genes related to apoptosis, cell cycle arrest, proliferation, differentiation, survival and transformation-related genes.
Publication Title
Hydroxytyrosol inhibits growth and cell proliferation and promotes high expression of sfrp4 in rat mammary tumours.
Sample Metadata Fields
Sex, Age, Specimen part, Treatment
View Samples- Rattus norvegicus
- 10 Downloadable Samples
- Affymetrix Rat Genome 230 2.0 Array (rat2302)
Description
The aim of this study was to compare the gene expression profile changes of DMBA-induced rat breast tumors after treatment with adriamycin. To this end, a cDNA microarray was performed (Affymetrixs Rat Genome 230 2.0 array). This gene expression study was carried out on the tumor biopsy samples prior to adriamycin treatment, and compared with matched tumor biopsy samples after completion of the adriamycin treatment schedule.
Publication Title
Hydroxytyrosol inhibits growth and cell proliferation and promotes high expression of sfrp4 in rat mammary tumours.
Sample Metadata Fields
Sex, Age, Specimen part, Treatment
View Samples- Rattus norvegicus
- 10 Downloadable Samples
- Affymetrix Rat Genome 230 2.0 Array (rat2302)
Description
The aim of this study was to compare the gene expression profile changes of DMBA-induced rat breast tumors from an initial stage to the moment of sacrifice. To this end, a cDNA microarray was performed (Affymetrixs Rat Genome 230 2.0 array). This gene expression study was carried out on the umor biopsy samples and compared with matched tumor biopsy samples once the study ended (7 weeks after initial biopsy).
Publication Title
Hydroxytyrosol inhibits growth and cell proliferation and promotes high expression of sfrp4 in rat mammary tumours.
Sample Metadata Fields
Sex, Age, Specimen part, Treatment
View Samples- Homo sapiens
- 36 Downloadable Samples
- Affymetrix Human Genome U219 Array (hgu219), Affymetrix Human Gene 1.1 ST Array (hugene11st)
Description
Interleukin-6 (IL-6) is an important growth factor for estrogen receptor-alpha (ER) positive breast cancer, and elevated serum IL-6 is associated with poor prognosis. We firstly demonstrated that pSTAT3 is the primary downstream IL-6 signaling pathway in ER-positive breast cancer, using ten different breast cancer cell lines. Three-dimensional cultures of these cell lines were also used to develop a 17-gene IL-6 specific gene signature that could be used to identify IL-6 driven disease. This signature included a variety of genes involved in immune cell function and migration, cell growth and apoptosis, and the tumor microenvironment. To further validate this IL-6 signature, we obtained 36 human ER-positive breast cancer tumor samples with matched serum for gene expression profiling and determination of an IL-6 pathway activation score (PAS). Patients with high IL-6 PAS were also enriched for elevated serum IL-6 (>=10 pg/ml). We then utilized a murine MCF-7 xenograft model to determine the role of IL-6 in ER-positive breast cancer and potential anti-IL-6 therapy in vivo. When IL-6 was administered in vivo, MCF-7 cells engrafted without the need for estrogen supplementation. Subsequently, we prophylactically treated mice at MCF-7 engraftment with an anti-IL-6 antibody (siltuximab), fulvestrant or combination therapy. Siltuximab alone was able to blunt MCF-7 engraftment. Similarly, when tumors were allowed to grow to 125 mm3 before treatment, siltuximab alone demonstrated tumor regressions in 90% (9/10) of tumors. Given the established role for IL-6 in ER+ breast cancer, this data demonstrates the potential for anti-IL-6 therapeutics.
Publication Title
Interleukin-6 is a potential therapeutic target in interleukin-6 dependent, estrogen receptor-α-positive breast cancer.
Sample Metadata Fields
Specimen part
View Samples- Escherichia coli
- 12 Downloadable Samples
- Affymetrix E. coli Genome 2.0 Array (ecoli2)
Description
We measured transcriptional changes resulting from overexpression or downregulation of the GTPase Obg.
Publication Title
Obg and Membrane Depolarization Are Part of a Microbial Bet-Hedging Strategy that Leads to Antibiotic Tolerance.
Sample Metadata Fields
No sample metadata fields
View Samples