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GSE1561
Homo sapiens
49 Downloadable Samples
Affymetrix Human Genome U133A Array (hgu133a)
Description
EORTC 10994 is a phase III clinical trial comparing FEC with ET in patients with large operable, locally advanced or inflammatory breast cancer (www.eortc.be). Frozen biopsies were taken at randomisation. RNA was extracted from 100um thickness of 14G core needle biopsies. Adjacent sections were tested by H&E to confirm >20% tumour cell content. 100 ng total RNA per chip were amplified using the Affymetrix small sample protocol (IVT then Enzo). 49 tumours were tested on Affymetrix U133A chips. The CEL files were quantile normalised together using rma. Clinical response data are not available yet.
Publication Title
Identification of molecular apocrine breast tumours by microarray analysis.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 2 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Branching morphogenesis in lung development is regulate by growth factor signaling. Wnt signaling is one of the important singnaling pathway that is required for progenitor maintainance. In the presence of CHIR99021, an agonist for the beta-catenin pathway of Wnt signaling, specific group of genes are upregulated in cultured lung epithelium.
Publication Title
Modulation of apical constriction by Wnt signaling is required for lung epithelial shape transition.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 38 Downloadable Samples
Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Feasibility of developing reliable gene expression modules from FFPE derived RNA profiled on Affymetrix arrays.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 6 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
The reliability of differential expression analysis on FFPE expression profiles from Affymetrix arrays is questionable, due to the wide range of percent-present values reported in studies which profiled FFPE samples on Affymetrix arrays. Moreover the validity of externally defined gene-modules in FFPE microarray expression profiles is unknown. Using eight breast cancer tumors with available frozen and FFPE samples, five sample-matched data sets were generated from different combination of Affymetrix arrays, amplification-and-labeling kit and sample preservation method. The reliability of differential expression analysis was investigated by developing de novo ER/HER2 pathway gene-modules from matched data sets and validating it on external data set using ROC analysis. Spearman's rank correlation coefficient of module scores between matched FFPE-frozen expression profiles was used to measure reliability of externally defined gene-modules in FFPE expression profiles. Independent of array/amplification-kit/sample preservation method used, de novo ER/HER2 gene-modules derived from all matching data sets showed similar prediction performance during independent validation (AUC range; ER: 0.92-0.95, HER2: 0.88-0.91), except for de novo HER2 gene-module derived from FFPE data set with 3'IVT kit (AUC: 0.67-0.72). Further not all gene-module based biological signals present in frozen expression profiles can be recovered from matching FFPE microarray expression profiles using the currently available FFPE specific sample preparation kits. The gene-module based biological signal extracted from FFPE RNA, using microarrays, may not be as reliable as that from their frozen counterpart, if the sample preparation protocol used with FFPE RNA failed to recover relevant genes involved in the biological signal.
Publication Title
Feasibility of developing reliable gene expression modules from FFPE derived RNA profiled on Affymetrix arrays.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 8 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
The reliability of differential expression analysis on FFPE expression profiles from Affymetrix arrays is questionable, due to the wide range of percent-present values reported in studies which profiled FFPE samples on Affymetrix arrays. Moreover the validity of externally defined gene-modules in FFPE microarray expression profiles is unknown. Using eight breast cancer tumors with available frozen and FFPE samples, five sample-matched data sets were generated from different combination of Affymetrix arrays, amplification-and-labeling kit and sample preservation method. The reliability of differential expression analysis was investigated by developing de novo ER/HER2 pathway gene-modules from matched data sets and validating it on external data set using ROC analysis. Spearman's rank correlation coefficient of module scores between matched FFPE-frozen expression profiles was used to measure reliability of externally defined gene-modules in FFPE expression profiles. Independent of array/amplification-kit/sample preservation method used, de novo ER/HER2 gene-modules derived from all matching data sets showed similar prediction performance during independent validation (AUC range; ER: 0.92-0.95, HER2: 0.88-0.91), except for de novo HER2 gene-module derived from FFPE data set with 3'IVT kit (AUC: 0.67-0.72). Further not all gene-module based biological signals present in frozen expression profiles can be recovered from matching FFPE microarray expression profiles using the currently available FFPE specific sample preparation kits. The gene-module based biological signal extracted from FFPE RNA, using microarrays, may not be as reliable as that from their frozen counterpart, if the sample preparation protocol used with FFPE RNA failed to recover relevant genes involved in the biological signal.
Publication Title
Feasibility of developing reliable gene expression modules from FFPE derived RNA profiled on Affymetrix arrays.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 8 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
The reliability of differential expression analysis on FFPE expression profiles from Affymetrix arrays is questionable, due to the wide range of percent-present values reported in studies which profiled FFPE samples on Affymetrix arrays. Moreover the validity of externally defined gene-modules in FFPE microarray expression profiles is unknown. Using eight breast cancer tumors with available frozen and FFPE samples, five sample-matched data sets were generated from different combination of Affymetrix arrays, amplification-and-labeling kit and sample preservation method. The reliability of differential expression analysis was investigated by developing de novo ER/HER2 pathway gene-modules from matched data sets and validating it on external data set using ROC analysis. Spearman's rank correlation coefficient of module scores between matched FFPE-frozen expression profiles was used to measure reliability of externally defined gene-modules in FFPE expression profiles. Independent of array/amplification-kit/sample preservation method used, de novo ER/HER2 gene-modules derived from all matching data sets showed similar prediction performance during independent validation (AUC range; ER: 0.92-0.95, HER2: 0.88-0.91), except for de novo HER2 gene-module derived from FFPE data set with 3'IVT kit (AUC: 0.67-0.72). Further not all gene-module based biological signals present in frozen expression profiles can be recovered from matching FFPE microarray expression profiles using the currently available FFPE specific sample preparation kits. The gene-module based biological signal extracted from FFPE RNA, using microarrays, may not be as reliable as that from their frozen counterpart, if the sample preparation protocol used with FFPE RNA failed to recover relevant genes involved in the biological signal.
Publication Title
Feasibility of developing reliable gene expression modules from FFPE derived RNA profiled on Affymetrix arrays.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 8 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
The reliability of differential expression analysis on FFPE expression profiles from Affymetrix arrays is questionable, due to the wide range of percent-present values reported in studies which profiled FFPE samples on Affymetrix arrays. Moreover the validity of externally defined gene-modules in FFPE microarray expression profiles is unknown. Using eight breast cancer tumors with available frozen and FFPE samples, five sample-matched data sets were generated from different combination of Affymetrix arrays, amplification-and-labeling kit and sample preservation method. The reliability of differential expression analysis was investigated by developing de novo ER/HER2 pathway gene-modules from matched data sets and validating it on external data set using ROC analysis. Spearman's rank correlation coefficient of module scores between matched FFPE-frozen expression profiles was used to measure reliability of externally defined gene-modules in FFPE expression profiles. Independent of array/amplification-kit/sample preservation method used, de novo ER/HER2 gene-modules derived from all matching data sets showed similar prediction performance during independent validation (AUC range; ER: 0.92-0.95, HER2: 0.88-0.91), except for de novo HER2 gene-module derived from FFPE data set with 3'IVT kit (AUC: 0.67-0.72). Further not all gene-module based biological signals present in frozen expression profiles can be recovered from matching FFPE microarray expression profiles using the currently available FFPE specific sample preparation kits. The gene-module based biological signal extracted from FFPE RNA, using microarrays, may not be as reliable as that from their frozen counterpart, if the sample preparation protocol used with FFPE RNA failed to recover relevant genes involved in the biological signal.
Publication Title
Feasibility of developing reliable gene expression modules from FFPE derived RNA profiled on Affymetrix arrays.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 8 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
The reliability of differential expression analysis on FFPE expression profiles from Affymetrix arrays is questionable, due to the wide range of percent-present values reported in studies which profiled FFPE samples on Affymetrix arrays. Moreover the validity of externally defined gene-modules in FFPE microarray expression profiles is unknown. Using eight breast cancer tumors with available frozen and FFPE samples, five sample-matched data sets were generated from different combination of Affymetrix arrays, amplification-and-labeling kit and sample preservation method. The reliability of differential expression analysis was investigated by developing de novo ER/HER2 pathway gene-modules from matched data sets and validating it on external data set using ROC analysis. Spearman's rank correlation coefficient of module scores between matched FFPE-frozen expression profiles was used to measure reliability of externally defined gene-modules in FFPE expression profiles. Independent of array/amplification-kit/sample preservation method used, de novo ER/HER2 gene-modules derived from all matching data sets showed similar prediction performance during independent validation (AUC range; ER: 0.92-0.95, HER2: 0.88-0.91), except for de novo HER2 gene-module derived from FFPE data set with 3'IVT kit (AUC: 0.67-0.72). Further not all gene-module based biological signals present in frozen expression profiles can be recovered from matching FFPE microarray expression profiles using the currently available FFPE specific sample preparation kits. The gene-module based biological signal extracted from FFPE RNA, using microarrays, may not be as reliable as that from their frozen counterpart, if the sample preparation protocol used with FFPE RNA failed to recover relevant genes involved in the biological signal.
Publication Title
Feasibility of developing reliable gene expression modules from FFPE derived RNA profiled on Affymetrix arrays.
Sample Metadata Fields
Specimen part
View Samples GSE35679- Homo sapiens
- 13 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Global gene expression of 13 frozen samples, 6 from typical and 7 from atypical surgically resected primary lung carcinoids
Publication Title
Gene expression profiling reveals GC and CEACAM1 as new tools in the diagnosis of lung carcinoids.
Sample Metadata Fields
Sex
View Samples- Homo sapiens
- 33 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Insulin-like growth factor receptor-1 (IGF-1R) inhibition could be a relevant therapeutic approach in small cell lung cancer (SCLC) given the importance of an IGF-1R autocrine loop and its role in DNA damage repair processes. We assessed IGF-1R and pAkt protein expression in 83 SCLC human specimens. The efficacy of R1507 (a monoclonal antibody directed against IGF-1R) alone or combined with cisplatin or ionizing radiation (IR) was evaluated in H69, H146 and H526 cells in vitro and in vivo. Innovative genomic and functional approaches were conducted to analyze the molecular behavior under the different treatment conditions. A total of 53% and 37% of human specimens expressed IGF-1R and pAkt, respectively. R1507 demonstrated single agent activity in H146 and H526 cells but not in H69 cells. R1507 exhibited synergistic effects with both Cisplatin and IR in vitro. The triple combination R1507-Cisplatin-IR led to a dramatic delay in tumor growth compared to Cisplatin-IR in H526 cells. Analyzing the apparent absence of antitumoral effect of R1507 alone in vivo, we observed a transient reduction of IGF-1R staining intensity in vivo, concomitant to the activation of multiple cell surface receptors and intracellular proteins involved in proliferation, angiogenesis and survival. Finally, we identified that the nucleotide excision repair pathway (NER) was mediated after exposure to R1507-CDDP and R1507-IR in vitro and in vivo. In conclusion, adding R1507 to the current standard Cisplatin-IR doublet reveals remarkable chemo- and radiosensitizing effects in selected SCLC models and warrants to be investigated in the clinical setting.
Publication Title
IGF-1R targeting increases the antitumor effects of DNA-damaging agents in SCLC model: an opportunity to increase the efficacy of standard therapy.
Sample Metadata Fields
Specimen part, Treatment
View Samples