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Homo sapiens
86 Downloadable Samples
Illumina HiSeq 2500
Description
The Androgen Receptor (AR) is the key-driving transcription factor in prostate cancer, tightly controlled by epigenetic regulation. To date, most epigenetic profiling has been performed in cell lines or limited tissue samples. To comprehensively study the epigenetic landscape, we complemented RNA-seq with ChIP-seq for AR and histone modification marks (H3K27ac, H3K4me3, H3K27me3) in 100 primary prostate carcinomas. Integrative molecular subtyping of the five data streams revealed three major subtypes of which two were clearly TMPRSS2-ERG dictated. Importantly, a third novel subtype was identified, with low AR chromatin binding and activity, even though the receptor was clearly expressed. While positive for neuroendocrine-hallmark genes, these tumors were copy number-neutral with low mutation burden, significantly depleted for genes characteristic of poor-outcome associated luminal B-subtype. We present a rich novel resource on transcriptional and epigenetic control in prostate cancer, revealing a tight control of gene regulation differentially dictated by AR over the three subtypes. Overall design: RNA-seq data for primary prostate carcinomas
Publication Title
Integrative epigenetic taxonomy of primary prostate cancer.
Sample Metadata Fields
Specimen part, Subject
View Samples- Mus musculus
- 143 Downloadable Samples
- Illumina HiSeq 2500, Illumina HiSeq 2000
Description
Cancer-associated inflammatory processes in the tumour microenvironment, as well as systemically, are strongly linked with poor disease outcome in cancer patients. For most human solid tumour types, high systemic neutrophil-to-lymphocyte ratios (NLR) are associated with increased metastasis and poor overall survival and recent experimental studies have demonstrated a causal relationship between neutrophils and metastasis formation. However, to date, the cancer cell-intrinsic mechanisms dictating the substantial heterogeneity in systemic neutrophilic inflammation between tumour-bearing hosts are largely unresolved. Using a panel of 16 distinct genetically engineered mouse models (GEMMs) for breast cancer, we demonstrate that tumour cell-intrinsic loss of p53 changes the phenotype and function of macrophages in the microenvironment, leading to activation of a systemic inflammatory cascade that drives neutrophil expansion. Mechanistically, p53 loss in cancer cells induces secretion of Wnt ligands that act in a paracrine fashion to stimulate IL-1b production from tumour-associated macrophages. Intratumoural IL-1ß production stimulates an inflammatory cascade leading to the systemic accumulation of neutrophils. Pharmacological and genetic blockade of cancer cell-derived Wnt secretion reverses IL-1ß expression by macrophages and subsequent systemic neutrophilic inflammation. Collectively, using pre-clinical mouse models for breast cancer, we demonstrate a novel mechanistic link between loss of p53 in cancer cells, Wnt ligand secretion and systemic immune activation. This illustrates the importance of cancer cell-intrinsic genetic aberrations in dictating cancer-associated inflammation. These insights set the stage for personalized immune intervention strategies for cancer patients. Overall design: In this study, gene expression profiles of tumours from genetically engineered mouse models (GEMMs) were analysed using RNA sequencing. Analysis was performed on bulk tumours of 10 GEMMs with different tissue-specific mutations driving tumorigenesis, totalling to 125 different tumours (n=5 or more per group). Subsequently, samples were grouped according to p53 status of the tumour (models containing Trp53 floxed alleles, or not) and comparisons were made between p53-KO and p53-WT tumours.
Publication Title
Loss of p53 triggers WNT-dependent systemic inflammation to drive breast cancer metastasis.
Sample Metadata Fields
Cell line, Subject
View Samples- Rattus norvegicus
- 10 Downloadable Samples
Affymetrix Rat Expression 230A Array (rae230a)
Description
Gene expression analysis in control and diabetic rats. Diabetes-induced erectile dysfunction in rat model of DM. 10 weeks of streptozotocin induced diabetes. F344 Rats.
Publication Title
Microarray analysis reveals novel gene expression changes associated with erectile dysfunction in diabetic rats.
Sample Metadata Fields
No sample metadata fields
View Samples
SRP029434- Homo sapiens
- 9 Downloadable Samples
- Illumina HiSeq 2000
Description
Using a chromatin regulator-focused shRNA library, we found that suppression of sex determining region Y-box 10 (SOX10) in melanoma causes resistance to BRAF and MEK inhibitors. To investigate how SOX10 loss leads to drug resistance, we performed transcriptome sequencing (RNAseq) of both parental A375 (Ctrl. PLKO) and A375-SOX10KD (shSOX10-1, shSOX10-2) cells. To ask directly whether SOX10 is involved indrug resistance in BRAF(V600E) melanoma patients, we isolated RNA from paired biopsies from melanoma patients (pre- and post- treatment) , that had gained BRAF or MEK inhibitor resistance . We performed RNAseq analysis to determine changes in transcriptome upon drug resistance. Overall design: Investigate genes regulated by SOX10 and differntial gene expression between pre- and post-treatment biopsies. We use short hairpin RNA to suppression SOX10 in A375 cells and cells were harvested with trizol reagent for RNA isolation. For paired biopsies (patient samples) we collected the first biopsy before the initiation of treatment and the second biopsy after drug resistance developed. RNA was isolated from FFPE samples and subjected for RNA sequencing.
Publication Title
Reversible and adaptive resistance to BRAF(V600E) inhibition in melanoma.
Sample Metadata Fields
Sex, Age, Specimen part, Cell line, Subject
View Samples- Homo sapiens
- 12 Downloadable Samples
- Affymetrix Human Genome U133A 2.0 Array (hgu133a2)
Description
Purpose: To identify the molecular phenotype of endothelial cells (EC) isolated from the unique vasculature of the corpus cavernosum.
Publication Title
Transcriptional profiling of human cavernosal endothelial cells reveals distinctive cell adhesion phenotype and role for claudin 11 in vascular barrier function.
Sample Metadata Fields
Sex, Specimen part
View Samples- Homo sapiens
- 9 Downloadable Samples
- IlluminaHiSeq2000
Description
Background and Aim: Fra-1 (Fos-related antigen-1) is a member of the AP1 (activator protein-1) family of transcription factors. We have recently shown that Fra-1 is necessary for breast cancer cells to metastasize in vivo, and that breast cancer outcome can be predicted by a classifier comprising genes that are expressed in a Fra-1-dependent fashion. Here, we show that Fra-1 plays an important role also in colon cancer progression. Methods: We compared proliferation rates of parental and Fra-1-depleted colon cancer cells in vitro under 2D, 3D, and attachment-free conditions and in vivo upon subcutaneous and intravenous injections into mice. We also compared RNA expression profiles of colon cancer cells with and without Fra-1 expression. Results: Fra-1 depletion impair colony outgrowth of human colon cancer cells in soft agar and in suspension, whereas it does not affect proliferation on 2D culture plates. Consistent with this, upon subcutaneous injection into mice, tumors formed by Fra-1-depleted colon cancer cells are only three times smaller than those produced by control cells. In contrast, when injected intravenously, Fra-1 depletion causes 200-fold reduction in tumor burden. Consistent with the more aggressive characteristics of Fra-1-proficient tumors, the prognosis of colon cancer patients can be predicted by a Fra-1 classifier generated by comparing RNA profiles of parental and Fra-1-depleted colon cancer cells. Conclusions: Our results demonstrate that Fra-1 is an important determinant of the metastatic potential of human colon cancer cells, and suggest that a Fra-1 classifier can be used as a prognostic predictor in colon cancer patients. Overall design: HT29 cell line, two shRNAs against Fra-1, one empty vector control, three biological replicates
Publication Title
Fra-1 is a key driver of colon cancer metastasis and a Fra-1 classifier predicts disease-free survival.
Sample Metadata Fields
No sample metadata fields
View Samples- Saccharomyces cerevisiae
- 29 Downloadable Samples
- Affymetrix Yeast Genome S98 Array (ygs98)
Description
Addition of 3 new arrays made from carbon limited chemostat of CENPK113-7D and 3 new arrays made from aerobic carbon limited chemostat of CENPK113-7D Complmentary data to the data of the serie GSE1723.
Publication Title
Exploiting combinatorial cultivation conditions to infer transcriptional regulation.
Sample Metadata Fields
No sample metadata fields
View Samples SRP038989- Mus musculus
- 6 Downloadable Samples
- Illumina HiSeq 2500
Description
The overall goal of our studies is to elucidate the cellular and molecular mechanism by which the transcription factor Casz1 functions in murine heart development. We established that Casz1 is expressed in myocardial progenitor cells beginning at E7.5 and in differentiated cardiomyocytes throughout development. We generated conditional Casz1 knockout mice to show that ablation of CASZ1 in Nkx2.5-positive cardiomyocytes leads to cardiac hypoplasia, ventricular septal defects and lethality by E13.5. To identify the pathways and networks by which Casz1 regulates cardiomyocyte development, we used RNA-Seq and identified genes involved in cell proliferation are upregulated in Casz1 mutants compared to wild-type littermates. We conclude that Casz1 is essential for cardiac development and has a pivotal role in regulating part of the cardiac transcriptional program. Overall design: 3 biological replicates of the two genotypes (Nkx2-5+/+,Casz1f/+ and Nkx2-5Cre/+,Casz1f/f) were used for RNA-seq to determine genes that are differentially expressed in the murine heart when Casz1 is mutated. Nkx2-5+/+,Casz1f/+ were used as wild-type controls for comparison.
Publication Title
Casz1 is required for cardiomyocyte G1-to-S phase progression during mammalian cardiac development.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 38 Downloadable Samples
Description
We profiled the transcriptome of cardiomyocytes from hiPSCs throughout differentiation and at a single cell level to identify subpopulations. We further studied on the transcription factors NR2F2, TBX5, and HEY2 in these subpopulations. Overall design: Cardiomyocytes derived from human induced pluripotent stem cells (hiPSC-CMs) have become a powerful tool for human disease modeling and therapeutic testing. However, their use remains limited by their immaturity and heterogeneity. To characterize the source of this heterogeneity, we performed bulk RNA-seq on hiPSCs undergoing differentiation into cardiomyocytes over an extended time course followed by single-cell RNA-seq at a later time point (day 30). These analyses identified novel single-cell populations, characterized by the distinct or overlapping expression of TBX5, NR2F2, HEY2, ISL1, JARID2, and HOPX transcription factors. Analysis of RNA-seq data from hiPSC-CMs both during differentiation in vitro and from human heart tissues suggests these transcription factors underlie physiologically distinct lineages. Using CRISPR genome editing and ChIP-seq, in conjunction with patch clamp, calcium imaging, CYTOF, and single-cell Western analysis, we now demonstrate that these transcription factors play an essential role in specification of early atrial (NR2F2) and late ventricular (HEY2) cardiomyocytes. We RNA-sequenced NR2F2, TBX5, HEY2 gene edited lines as well as day 30 hiPSC-CMs overexpressing NR2F2, TBX5, and HEY2. These new targets, sequencing data, and methods provide a platform for improved investigation of in vitro cardiac heterogeneity.
Publication Title
Defining human cardiac transcription factor hierarchies using integrated single-cell heterogeneity analysis.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 8 Downloadable Samples
- Illumina Genome Analyzer IIx
Description
Clinicians need additional metrics for predicting quality of human oocytes for IVF procedures. Human polar bodies reflect the oocyte transcript profile. Quantitation of polar body mRNAs could allow for both oocyte ranking and embryo preferences in IVF applications. The transcriptome of a polar body has never been reported, in any organism. Overall design: Eight total samples. There are 2 biological replicates of the following four conditions: pooled oocytes and their sister polar bodies and a single oocyte and its sister polar body.
Publication Title
The transcriptome of a human polar body accurately reflects its sibling oocyte.
Sample Metadata Fields
Specimen part, Subject
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