GEO DataSets

(Submitter supplied) In psychiatric disorders, common and rare genetic variants cause widespread dysfunction of cells and their interactions, especially in the prefrontal cortex, giving rise to psychiatric symptoms. To better understand these processes, we traced the effects of common and rare genetics, and cumulative disease risk scores, to their molecular footprints in human cortical single-cell types. We demonstrated that examining gene expression at single-exon resolution is crucial for understanding the cortical dysregulation associated with diagnosis and genetic risk derived from common variants. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL5188

169 Samples

Download data: CEL

(Submitter supplied) Induced cellular reprogramming to the pluripotent state offers a novel stem cell source for autologous transplantation. While recent studies have explored the role of factors required for induced pluripotent stem cell (iPSC) induction, the cellular and molecular basis of reprogramming from human fibroblasts remains elusive. Here, we have identified a subset of human dermal-derived fibroblasts that shares hallmark molecular and epigenetic features with pluripotent cells. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL570 GPL5188

6 Samples

Download data: CEL

(Submitter supplied) Our previous studies of proteomic-coupled-network analysis of AR protein interaction complexes (Paliouras et al., Integrative Biology, 2011) identified a number of proteins involved in RNA metabolism, specifically alternative RNA splicing. We selected two interacting RNA splicing proteins, SAM68 and DDX5 to examine RNA splicing events in prostate cancer (PCa). This analysis suggests a much more robust effect on RNA splicing with AR dictating either an exon-inclusion or -exclusion pathway. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL5188

36 Samples

Download data: CEL

(Submitter supplied) Exon Level Expression Profiling of HeLa cells depleted of DNMT1 by 2 independent siRNAs In HeLa cells where depletion of DNMT1 was sufficient to cause reduced levels of DNA methylation inside the body of CD44 and reduced usage of CD44 variant exons, without affecting splicing factors regulating CD44.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL5188

9 Samples

Download data: CEL, CHP, XLS

(Submitter supplied) Inflammatory Breast Cancer (IBC) is the most aggressive form of breast carcinoma characterized by the rapid onset of inflammatory signs. The molecular fingerprint for this rare, severe and unique clinical entity is still not elucidated. The goal of the present work was to detect both gene expression levels and alternate RNA splice variants specific to IBC. Experimental Design: In order to identify differentially expressed genes and splicing events, we performed splice-sensitive array profiling using Affymetrix Exon Array and quantitative RT-PCR analyses in a large series of 177 IBC compared to 183 non-IBC. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL5175 GPL5188

122 Samples

Download data: CEL

(Submitter supplied) KRAS is the most frequently mutated oncogene in human cancer, but its therapeutic targeting remains challenging. Here, we report a synthetic lethal screen with a library of deubiquitinases and identify USP39, which encodes an essential splicing factor, as a critical gene for the viability of KRAS-dependent cells. We show that the essentiality of USP39 for these cells is based on its critical role in splicing regulation, as splicing fidelity inhibitors also decrease preferentially the proliferation rate of KRAS-active cells. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL5188

4 Samples

Download data: CEL

(Submitter supplied) Intracellular Tat101 deregulated the expression of spliceosome core components, such as SF3B2, SF3A1, SFPQ, PCBP1, SYNCRIP, YBX1 and HSP8A/HSP7C, and thus likely the splicing pathway. Viral splicing experiments showed that Tat101 favored the expression of viral unspliced RNA, which are used at the late steps of the viral cycle, rather than spliced RNAs allowing the progression of HIV-1 replication.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL5188 GPL5175

24 Samples

Download data: CEL

(Submitter supplied) We postulated that specific differences in alternative splicing/exon usage in immune blood cells may be present in ASD boys, and this might differ in ASD boys with large total cerebral volumes (ASD_LTCV) versus ASD boys with normal total cerebral volumes (ASD_NTCV). Thus, we compared ASD and ASD sub-groups related to total cerebral volume to typically developing (TD) controls.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL5188

50 Samples

Download data: CEL

(Submitter supplied) Transcriptome analysis of post-mortem brain tissue specimens from three brain regions (BRs), entorinal, temporal and frontal cortices, of 71 Japanese brain-donor subjects to identify genes relevant to the expansion of neurofibrillary tangles. In total, 213 brain tissue specimens (= 71 subjects × 3 BRs) were involved in this study. The spreading of neurofibrillary tangles (NFTs), intraneuronal aggregates of highly phosphorylated microtubule-associated protein tau, across the human brain is correlated with the cognitive severity of Alzheimer’s disease (AD). more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL5188 GPL5175

426 Samples

Download data: CEL, CHP, XLSX

(Submitter supplied) Exon expression profiling was performed on 37 clinical DLBCL samples and subsequently analyzed using alternative splice analysis of vairance (asANOVA) implemented in Partek Genomics Suite in order to identify alternative spliced genes. Diffuse large B-cell lymphoma (DLBCL) is a very heterogeneous malignant disease with diverse clinical presentation, outcome, and pathogenic mechanism. In order to better risk stratify patients there is a current need to find and validate new biomarkers of the disease. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL5188

37 Samples

Download data: CEL

(Submitter supplied) The dataset consists of 266 NCCN very low/low or favorable-intermediate risk PCa patients who underwent diagnostic prostate biopsy between 2000 and 2014 and were treated with RP in six community or academic practices: University of Calgary, Cedars-Sinai, Spectrum Health, Cleveland Clinic, MD Anderson Cancer Center and Johns Hopkins. All patients had complete tumor pathology from biopsy and prostatectomy. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL5188

266 Samples

Download data: CEL, CSV

(Submitter supplied) We performed exon array analysis to define and compare the transcriptomic changes, in terms of splicing and gene expression profilings, occurring in human neuroblastoma cells upon knocking down TDP-43 and FUS RNA-binding proteins (RBP), with the final aim to unravel the biological role of these RBPs in neuronal cells.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL5188 GPL5175

18 Samples

Download data: CEL

(Submitter supplied) The ultraconserved RNA TUC338 is expressed in hepatocellular cancer and can modulate cell proliferation. Details are provided in Braconi et al,Proc Natl Acad Sci U S A. 2011 Jan 11;108(2):786-91. In this analysis, we knocked down TUC338 in HepG2 cells and analyzed gene expression.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL5188

2 Samples

Download data: CEL

(Submitter supplied) Here we show that depletion of the homologous non-classical serine-arginine-rich (SR) splicing factors Btf (BCLAF1) and TRAP150 causes mitotic defects. We propose that, in addition to their previously reported roles in maintaining mRNA distribution, Btf and TRAP150 control abundance of transcripts encoding mitotic regulators thereby affecting mitotic progression in human cells.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL5188

16 Samples

Download data: CEL, CHP

(Submitter supplied) Chinese lung SCC adjacent normal sample exon-level expression

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL5188

5 Samples

Download data: CEL

(Submitter supplied) Chinese lung squamous cell carcinomas exon-level expression

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL5188

65 Samples

Download data: CEL

(Submitter supplied) Primary glioblastoma (GBM) cultures vary with respect to differentiation competency. We sought to identify putative transcription factors necessary for the differentiation of GBM cultures. In this dataset, we include expression data obtained from 2 human-fetal neural stem cell (HF-NS) cultures and 2 GBM stem cell (GSC) cultures. We assessed changes in gene expression from 3 timepoints during an in vitro differentiation protocol.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL5188

12 Samples

Download data: CEL

(Submitter supplied) Alternative splicing is a key event to human transcriptome and proteome diversity and complexity. Recent evidence suggests that pancreatic cancer might possess particular patterns of splice variation that influence the function of individual genes contributing to tumour progression in this disease. The identification of new pancreatic cancer-associated splice variants would offer opportunities for novel diagnostics and potentially also represent novel therapeutic targets. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL5188

35 Samples

Download data: CEL

(Submitter supplied) Chinese lung ADC adjacent normal sample exon-level expression

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL5188

10 Samples

Download data: CEL

(Submitter supplied) Chinese lung adenocarcinomas exon-level expression

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL5188

78 Samples

Download data: CEL