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GSE135427
Homo sapiens
4 Downloadable Samples
Illumina HumanHT-12 V4.0 expression beadchip
Description
To elucidate the KDM4B regulated transcriptomes in ER-positive breast cancer cells we assessed global gene expression changes in KDM4B-depleted MCF-7 cells by microarray analysis using the Illumina Human HT12 Version 4 BeadChip array. Differentially expressed genes were compared with KDM3A and FOXA1 regulated transcriptomes. We identified 229 genes co-regulated by all three enzymes and that co-regulated genes were involved in cell cycle processes. We identified that 53% and 48% of KDM4B-regulated genes were also regulated by KDM3A and FOXA1, with co-regulatory gene signatures being involved with estrogen response signatures and cell proliferation. We also identified that depletion of KDM3A and KDM4B together inhibits ER-target gene expression and ER-positive breast cancer cell growth more than depletion of either gene on its own.
Publication Title
The Histone Demethylase Enzymes KDM3A and KDM4B Co-Operatively Regulate Chromatin Transactions of the Estrogen Receptor in Breast Cancer.
Sample Metadata Fields
Specimen part, Cell line
View Samples- Macaca mulatta
- 11 Downloadable Samples
- Affymetrix Rhesus Macaque Genome Array (rhesus)
Description
The elaboration of a quality oocyte is integrally linked to the correct developmental progression of cumulus cell phenotype. In humans and non-human primates, oocyte quality is diminished with in vitro maturation. To determine the changes in gene expression in rhesus monkey cumulus cells (CC) that occur during the final day prior to oocyte maturation and how these changes differ between in vitro and in vivo maturation (IVM and VVM), we completed a detailed comparison of transcriptomes using the Affymetrix gene array. We observe a large number of genes differing in expression when comparing IVM-CC and VVM-CC directly, but a much larger number of differences comparing the transitions from the pre-oocyte maturation to post- IVM and post-VVM state. We observe a truncation or delay in the normal pattern of gene regulation, but also remarkable compensatory changes in gene expression during IVM. Among the genes affected in cumulus cells by IVM are those that contribute to productive cell-cell interactions between cumulus cell and oocyte and between cumulus cells. Numerous genes involved in lipid metabolism are incorrectly regulated during IVM, and the synthesis of sex hormones appears not suppressed during IVM. We identify a panel of 24 marker genes, the expression of which should provide the foundation for understanding how IVM can be improved, for monitoring IVM conditions, and for diagnosing oocyte quality.
Publication Title
Extensive effects of in vitro oocyte maturation on rhesus monkey cumulus cell transcriptome.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 6 Downloadable Samples
Illumina HiSeq 2500
Description
Development of a novel CRISPR-derived cell line which is a derivative of CWR22Rv1 cells, called CWR22Rv1-AR-EK, that has lost expression of FL-AR, but retains all endogenous AR-Vs. AR-Vs act unhindered by loss of FL-AR to drive cell growth and expression of androgenic genes. Global transcriptomics demonstrate that AR-Vs drive expression of a cohort of DNA damage response genes and depletion of AR-Vs sensitizes cells to ionizing radiation. Overall design: Transcriptomic profile (mRNA) of AR splice variants in CWR22Rv1 AR-EK cells was generated by deep sequencing, in triplicate, using Illumina HiSeq 2500.
Publication Title
A novel CRISPR-engineered prostate cancer cell line defines the AR-V transcriptome and identifies PARP inhibitor sensitivities.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Homo sapiens
- 20 Downloadable Samples
- Affymetrix Human Genome U133A Array (hgu133a)
Description
Normal primary thyroid cells were incubated with vehicle, 100 IU/ml IFN-gamma, 50 IU/ml IL1-beta, or a combination of both IFN-gamma and IL1-beta for 24 or 72 hours. The experiment was repeated 5 times using thyroid cells from 5 different patients. RNA expression was analyzed using Affymetrix HG_U133A arrays for 3 of the thyroids, and HG_U133A_2.0 (small version of HG_U133A) arrays for 2 of the thyroids.
Publication Title
Microarray analysis of cytokine activation of apoptosis pathways in the thyroid.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 62 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Human samples of 33 adrenocortical carcinomas, 22 adrenocortical adenomas, and 10 normal adrenal cortex samples, each from a different patient, had mRNA assays performed using Affymetrix HG_U133_plus_2 arrays, with 54675 probe-sets. We note that the same array data is in GEO series GSE33371, where we assayed the cancer samples for Beta-catenin staining or mutation, and make new comparisons based on those assays.
Publication Title
Molecular classification and prognostication of adrenocortical tumors by transcriptome profiling.
Sample Metadata Fields
Sex, Age
View Samples- Homo sapiens
- 99 Downloadable Samples
- Affymetrix Human Genome U133A Array (hgu133a)
Description
Human samples of various thyroid carcinomas, adenomas, and normals, each from a different patient, had mRNA assays performed using Affymetrix HG_U133A arrays, with 22283 probe-sets. The 99 samples consisted of 4 normals, 10 follicular adenomas, 13 follicular carcinomas, 7 oncocytic adenomas, 8 oncocytic carcinomas, 51 papillary carcinomas (each typed as having classical, follicular or tall cell morphology), 4 anaplastic carcinomas, and 2 medullary carcinomas. Interesting additional information on common mutations are provided including RAS mutation, BRAF mutation, RET/PTC rearrangements, and PAX8/PPARG translocations. Details of those assays are provided in our linked publications, as well as additional details on the specific mutations in a few special cases. No survival data is provided. Information for 93 of the 99 samples was previously made available on the web. The anaplastic and medullary carcinoma data were not previously shared. A supplementary Excel spreadsheet holding the same processed data as the series matrix file is provided and is more compact. The raw (.CEL) files are also provided.
Publication Title
Molecular classification of papillary thyroid carcinoma: distinct BRAF, RAS, and RET/PTC mutation-specific gene expression profiles discovered by DNA microarray analysis.
Sample Metadata Fields
Specimen part
View Samples- Rattus norvegicus
- 12 Downloadable Samples
- Affymetrix Rat Expression 230A Array (rae230a)
Description
Effects of hyperglycaemia and genetic background differences on renal gene expression
Publication Title
Comparative analysis of methods for gene transcription profiling data derived from different microarray technologies in rat and mouse models of diabetes.
Sample Metadata Fields
Sex, Age, Specimen part, Disease, Subject
View Samples- Rattus norvegicus
- 17 Downloadable Samples
- Illumina ratRef-12 v1.0 expression beadchip
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
MicroRNA-125a is over-expressed in insulin target tissues in a spontaneous rat model of Type 2 Diabetes.
Sample Metadata Fields
Sex, Age, Specimen part
View Samples- Rattus norvegicus
- 17 Downloadable Samples
- Illumina ratRef-12 v1.0 expression beadchip
Description
Type 2 diabetes (T2D) is characterized by hyperglycaemia and defects in insulin secretion and action at target tissues. Using the Illumina RatRef-12 v1.0 array, gene expression was assessed in two insulin-target tissues (liver and adipose tissue) from seven-month-old spontaneously diabetic (Goto-Kakizaki [GK]) and non-diabetic (Brown-Norway [BN]) rats. This study was performed in parallel with miRNA expression profiling of the same rats.
Publication Title
MicroRNA-125a is over-expressed in insulin target tissues in a spontaneous rat model of Type 2 Diabetes.
Sample Metadata Fields
Sex, Age, Specimen part
View Samples- Mus musculus
- 22 Downloadable Samples
- Affymetrix Mouse Expression 430B Array (moe430b), Affymetrix Mouse Expression 430A Array (moe430a)
Description
Effect of high fat diet feeding on gene expression
Publication Title
Subtle metabolic and liver gene transcriptional changes underlie diet-induced fatty liver susceptibility in insulin-resistant mice.
Sample Metadata Fields
Sex, Age, Specimen part, Subject
View Samples