Filters
Technology
Platform
GSE39397
Homo sapiens
49 Downloadable Samples
Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2), Affymetrix HT HG-U133+ PM Array Plate (hthgu133pluspm)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Dependency of colorectal cancer on a TGF-β-driven program in stromal cells for metastasis initiation.
Sample Metadata Fields
Specimen part, Disease, Disease stage, Treatment, Subject
View Samples- Homo sapiens
- 23 Downloadable Samples
Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
The survival of isolated metastatic cells and expansion into macroscopic tumour has been recognized as a limiting step for metastasis formation in several cancer types yet the determinants of this process remain largely uncharacterized. In colorectal cancer (CRC), we identify a transcriptional programme in tumour-associated stromal cells, which is intimately linked to a high risk of developing recurrent disease after therapy. A large proportion of CRCs display mutational inactivation of the TGF-beta pathway but paradoxically they are characterized by high TGF-beta production. In these tumours, TGF-beta instructs a transcriptional programme in stromal cells, which confers a high risk of developing metastatic disease.
Publication Title
Dependency of colorectal cancer on a TGF-β-driven program in stromal cells for metastasis initiation.
Sample Metadata Fields
Specimen part, Disease, Disease stage, Subject
View Samples- Homo sapiens
- 22 Downloadable Samples
- Affymetrix HT HG-U133+ PM Array Plate (hthgu133pluspm), Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
The survival of isolated metastatic cells and expansion into macroscopic tumour has been recognized as a limiting step for metastasis formation in several cancer types yet the determinants of this process remain largely uncharacterized. In colorectal cancer (CRC), we identify a transcriptional programme in tumour-associated stromal cells, which is intimately linked to a high risk of developing recurrent disease after therapy. A large proportion of CRCs display mutational inactivation of the TGF-beta pathway but paradoxically they are characterized by high TGF-beta production. In these tumours, TGF-beta instructs a transcriptional programme in stromal cells, which confers a high risk of developing metastatic disease.
Publication Title
Dependency of colorectal cancer on a TGF-β-driven program in stromal cells for metastasis initiation.
Sample Metadata Fields
Disease, Disease stage, Subject
View Samples- Homo sapiens
- 4 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
The survival of isolated metastatic cells and expansion into macroscopic tumour has been recognized as a limiting step for metastasis formation in several cancer types yet the determinants of this process remain largely uncharacterized. In colorectal cancer (CRC), we identify a transcriptional programme in tumour-associated stromal cells, which is intimately linked to a high risk of developing recurrent disease after therapy. A large proportion of CRCs display mutational inactivation of the TGF-beta pathway but paradoxically they are characterized by high TGF-beta production. In these tumours, TGF-beta instructs a transcriptional programme in stromal cells, which confers a high risk of developing metastatic disease.
Publication Title
Dependency of colorectal cancer on a TGF-β-driven program in stromal cells for metastasis initiation.
Sample Metadata Fields
Specimen part, Treatment
View Samples GSE79660- Homo sapiens
- 12 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
These data show distinct interactions between these two drugs on CLL cells in vitro with an ex vivo treatment
Publication Title
Lenalidomide Induces Interleukin-21 Production by T Cells and Enhances IL21-Mediated Cytotoxicity in Chronic Lymphocytic Leukemia B Cells.
Sample Metadata Fields
Specimen part, Treatment, Subject
View Samples- Homo sapiens
- 45 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Therapies targeting the type I insulin-like growth factor receptor (IGF-1R) have not been developed with predictive biomarkers to identify tumors with receptor activation. We have previously shown that the insulin receptor substrate (IRS) adaptor proteins are necessary for linking IGF1R to downstream signaling pathways and the malignant phenotype in breast cancer cells. The purpose of this study was to identify gene expression profiles downstream of IGF1R and its two adaptor proteins. IRS-null breast cancer cells (T47D-YA) were engineered to express IRS-1 or IRS-2 alone and their ability to mediate IGF ligand-induced proliferation, motility, and gene expression determined. Global gene expression signatures reflecting IRS adaptor specific and primary vs. secondary ligand response were derived (Early IRS-1, Late IRS-1, Early IRS-2 and Late IRS-2) and functional pathway analysis examined. IRS isoforms mediated distinct gene expression profiles, functional pathways, and breast cancer subtype association. For example, IRS-1/2-induced TGFb2 expression and blockade of TGFb2 abrogated IGF-induced cell migration. In addition, the prognostic value of IRS proteins was significant in the luminal B breast tumor subtype. Univariate and multivariate analyses confirmed that IRS adaptor signatures correlated with poor outcome as measured by recurrence-free and overall survival. Thus, IRS adaptor protein expression is required for IGF ligand responses in breast cancer cells. IRS-specific gene signatures represent accurate surrogates of IGF activity and could predict response to anti-IGF therapy in breast cancer.
Publication Title
Insulin Receptor Substrate Adaptor Proteins Mediate Prognostic Gene Expression Profiles in Breast Cancer.
Sample Metadata Fields
Cell line
View Samples- Mus musculus
- 157 Downloadable Samples
NextSeq 500
Description
Purpose: The goals of this study are to establish a roadmap of XCI and compare the transcriptomes of WT and Rlim KO embryos during X chromosome inactivation. Methods: mRNA profiles of 175 preimplantation embryos WT and KO for Rlim were elucidated by RNA-seq at various stages. Trophoblasts isolated from blastocyst outgrowths were also included. The sequence reads that samples where gender could be determined and that passed quality filters were analyzed at the level of autosomes, X xhromosomes as well as single genes. Results: Using single cell RNA-seq technology on 175 whole preimplantation embryos, we obtained about 2.95 million sequence reads per sample. Reads were normalized to autosomal gene expression. Gender of each embryo was determined by expression of Y-linked genes and Xist. Data analysis showed normal expression profiles of marker genes for epiblast and trophoblast cell types during preimplantation development. Comparing Xist expression profiles in embryos WT and KO shows that Rlim is not required for initiation of Xist transcription but for upregulation of Xist expression. Moreover, our results identify two waves of XCI during preimplantation development: One that occurs at Morula stages that is Rlim-independent and one at blastocyst stages that in dependent on Rlim. Conclusions: Our study represents the first detailed mouse preimplantation transcriptome. Our results show that Rlim is required for a second wave of imprinted XCI that occurs in female embryos at blastocyst stages. Overall design: Global mRNA profiles of whole preimplantation embryos were generated by deep sequencing.
Publication Title
Regulation of X-linked gene expression during early mouse development by <i>Rlim</i>.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 141 Downloadable Samples
- NextSeq 500
Description
Purpose: The goals of this study are to establish a dynamic roadmap of imprinted X chromosome inactivation and the role of Xist by elucidation of the transcriptome of Xist KO embryos during mouse preimplantation development. Methods: mRNA profiles of the preimplantation embryos WT and KO for Xist were elucidated by RNA-seq at various stages. Trophoblasts isolated from blastocyst outgrowths were also included. The sequence reads for samples where gender could be determined and that passed quality filters were analyzed at the level of autosomes, X chromosome as well as single genes. Results: Female embryos fail to silence the X chromosome at late preimplantation development. General autosomal gene expression is not affected in embryos lacking Xist. Conclusions: Xist is crucial for iXCI. In preimplantation embryos, the main in vivo function of Xist is to regulate iXCI in females. Overall design: Global mRNA profiles of single preimplantation embryos were generated by deep sequencing.
Publication Title
Regulation of X-linked gene expression during early mouse development by <i>Rlim</i>.
Sample Metadata Fields
Sex, Specimen part, Subject
View Samples- Mus musculus
- 12 Downloadable Samples
- NextSeq 500
Description
The transcriptomes of differentiated and undifferentiated E14 (male), Pgk12.1 (female; WT) and Pgk12.1 with a KO of Rlim (RlimKO) were elucidated and examined for differences in X chromosome inactivation. No significant differences between wt and RlimKO with respect to Xist expression and global X-silencing was detected. Results confirm that Rlim is not required for XCI in female ESCs. Overall design: Transciptomes of female WT (Pgk12.1) and female RlimKO ESCs were compared to those of male ESCs (E14). State of XCI in undifferentiated and differentiated ESCs was determined by comparing expression of Xist and expression of X-linked genes female versus male.
Publication Title
Rlim-Dependent and -Independent Pathways for X Chromosome Inactivation in Female ESCs.
Sample Metadata Fields
Sex, Specimen part, Cell line, Subject
View Samples- Mus musculus
- 8 Downloadable Samples
- NextSeq 500
Description
Purpose: The goals of this study are to establish a dynamic roadmap of imprinted X chromosome inactivation and the role of Xist by elucidation of the transcriptome of Xist KO embryos during mouse preimplantation development Methods: mRNA profiles of the preimplantation embryos WT and KO for Xist were elucidated by RNA-seq at various stages. Trophoblasts isolated from blastocyst outgrowths were also included. The sequence reads that samples where gender could be determined and that passed quality filters were analyzed at the level of autosomes, X chromosome as well as single genes. Effects of genetic background on the kinetics of iXCI was evaluated by RNA-seq on E3.5 embryos with a hybrid C57BL/6 x Cast background. Results: Female embryos fail to silence the X chromosome at late preimplantation development. General autosomal gene expression is not affected in embryos lacking Xist. Conclusions: Xist is crucial for iXCI. In preimplantation embryos the main in vivo function of Xist is to regulate iXCI in females. Genetic background does not significantly influence kinetics of iXCI. Overall design: Global mRNA profiles of single preimplantation embryos were generated by deep sequencing.
Publication Title
Regulation of X-linked gene expression during early mouse development by <i>Rlim</i>.
Sample Metadata Fields
Sex, Cell line, Subject
View Samples