E-GEOD-52463
Ontology highlight
ABSTRACT:
OTHER RELATED OMICS DATASETS IN: PRJNA229054
DISEASE(S): Idiopathic Pulmonary Fibrosis,Normal
PROVIDER: E-GEOD-52463 | ExpressionAtlas | 2019-05-14
REPOSITORIES: ExpressionAtlas
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| E-GEOD-52463-analysis-methods.tsv | Tabular | |||
| E-GEOD-52463-analytics.tsv | Tabular | |||
| E-GEOD-52463-analytics.tsv.undecorated | Tabular | |||
| E-GEOD-52463-analytics.tsv.undecorated.unrounded | Tabular | |||
| E-GEOD-52463-analytics.tsv.unrounded | Tabular |
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Similar Datasets
Project description:Transcriptome analysis reveals differential splicing events in IPF lung tissue
| PRJNA229054 | ENA
Project description:<p>Version 1</p> <p>Whole genome sequencing was applied to tumor and adjacent normal lung tissue in an individual non-small-cell lung cancer patient. We present an analysis of somatic changes identified throughout the tumor genome, including single-nucleotide variants, copy number variants, and large-scale chromosomal rearrangements. Over 50,000 high-confidence single-nucleotide variants were identified, revealing evidence of substantial smoking-related DNA damage as well as distinct mutational pressures within the tumor resulting in uneven distribution of somatic mutations across the genome.</p> <p>Version 2</p> <p>Lung cancer is a highly heterogeneous disease in terms of both underlying genetic lesions and response to therapeutic treatments. We performed deep whole genome sequencing and transcriptome sequencing on 19 lung cancer cell lines and 3 lung tumor/normal pairs. Overall, our data show that cell line models exhibit similar mutation spectra to human tumor samples. Smoker and never-smoker cancer samples exhibit distinguishable patterns of mutations. A number of epigenetic regulators are frequently altered by mutations or copy number changes. A systematic survey of splice-site mutations identified over 100 splice site mutations associated with cancer specific aberrant splicing, including mutations in several known cancer-related genes. Differential usages of splice isoforms were also studied. Taken together, these data present a comprehensive genomic landscape of a large number of lung cancer samples and further demonstrate that cancer specific alternative splicing is a widespread phenomenon that has potential utility as therapeutic biomarkers.</p>
| phs000299 | dbGaP
Project description:Changes in alternative splicing are associated with several pathological conditions, including cancer. Microarrays strategies, which allow for the characterization of thousands of alternative splice forms in a single test, can be applied to identify differential alternative splicing events. In this study, a novel splice array platform was developed, including the design of a high-density oligonucleotide array, a labeling procedure, and an algorithm to identify splice events. The array consists of exon probes and thermodynamically balanced junction probes. Suboptimal probes are tagged and considered in the final analysis. An unbiased labeling protocol was developed using random primers. The algorithm used to distinguish changes in expression from changes in splicing was calibrated using internal non-spliced control sequences. The performance of this splice array was first validated with artificial constructs for CDC6, VEGF, and PCBP4 isoforms. The platform was then applied to the analysis of differential splice forms for 8000 genes in lung cancer samples compared to matched normal lung tissue. The expression of lung cancer-associated splice isoforms was validated by RT-PCR. Overexpression of splice isoforms was identified for genes encoding CEACAM1, FHL-1, MLPH, and SUSD2. None of these splicing isoforms had been previously associated with lung cancer. In conclusion, this highly accurate methodology enables the detection of alternative splicing events in complex biological samples, providing a powerful tool to identify novel diagnostic and prognostic biomarkers for cancer and other pathologies. 20 normal/tumor paired specimens. Tumor samples are from non-small cell lung cancer (NSCLC) whereas normals are from adjacent normal lung tissue.
2010-06-21 | E-GEOD-18346 | biostudies-arrayexpress
Project description:Objectives: Idiopathic pulmonary fibrosis (IPF) is a complex disease in which a multitude of proteins and networks are disrupted. Interrogation of genome-wide transcription through RNA sequencing (RNA-Seq) enables the determination of genes whose differential expression is most significant in IPF, as well as the detection of alternative splicing events which are not easily observed with traditional microarray experiments. Methods: Messenger RNA extracted from 8 IPF lung samples and 7 healthy controls was sequenced on an Illumina HiSeq. Analysis of differential expression and exon usage was performed using Bioconductor packages. The gene periostin was selected for validation of alternative splicing by quantitative PCR, and pathway analysis was performed to determine enrichment for differentially expressed and spliced genes. Results: There were 873 genes differentially expressed in IPF (FDR 5%), and 440 unique genes had significant differential splicing events (FDR 5%). In particular, cassette exon 21 of the gene periostin was significantly more likely to be spliced out in IPF samples (adj pval = 2.06e-09), and this result was confirmed by qPCR (Wilcoxon pval = 3.11e-4). We also found that genes close to SNPs in the discovery set of a recent IPF GWAS were enriched for genes differentially expressed in our data, including genes like mucin5B and desmoplakin which have been previously associated with IPF. Conclusions: There is significant differential splicing and expression in IPF lung samples as compared with healthy controls. We found a strong signal of differential cassette exon usage in periostin, an extracellular matrix protein whose increased gene-level expression has been associated with IPF and its clinical progression, but for which differential splicing has not been studied in the context of IPF. Our results suggest that alternative splicing of periostin and other genes may be involved in the pathogenesis of IPF. mRNA sequencing of 8 IPF and 7 control lung tissue samples.
2014-03-27 | E-GEOD-52463 | biostudies-arrayexpress
Project description:The transcriptome-wide response of breast and lung cancer cells to chronic hypoxia was analyzed. Differential gene expression, alternative splicing and circRNA levels were quantified.
2020-04-21 | GSE131378 | GEO
Project description:We report the application of bulk RNA sequencing to RNA extracted from lung tissue and magnetic bead isolated EpCAM+ lung epithelial cells and CD45+ lung immune cells from mice. Heterozygous serine palmitory transferase subunit 2 , Sptlc2+/- (SPT) and Sptlc2+/+ controls (WT) mice were included. Differential gene expression analysis reveals genes within the sphingolipid synthesis pathway are similarly expressed in the lung and lung epithelial cells of RV infected WT mice and SPT mice (both infected and uninfected).
2021-11-20 | GSE189056 | GEO
Project description:High-throughput RNA sequencing (RNA-Seq) has enabled accurate gene discovery and expression estimation, but robust differential analysis of gene and transcript abundances has proven difficult. We present a new algorithm, implemented in the freely available tool Cuffdiff, which integrates transcript-level expression estimation with a method to control for variability across replicate samples. Cuffdiff robustly identifies differentially regulated isoforms and genes and reveals differential splicing or promoter-preference changes. We demonstrate the accuracy of our approach through differential analysis of lung fibroblasts in response to loss of the developmental transcription factor HOXA1 and uncover a critical role for this gene in the maintenance of adult cells. We show that HOXA1 is required for lung fibroblast and HeLa cell cycle progression, and loss of HOXA1 results in significant expression level changes in thousands of individual transcripts, along with isoform switching events in key regulators of the cell cycle. Lung Fibroblasts were transfected with either a HOXA1 directed siRNA pool or a scramble non-targeting siRNA control. RNA was collected 48 hours after transfection and changes in gene expression were assayed for using Agilent microarrays.
2012-12-11 | E-GEOD-37703 | biostudies-arrayexpress
Project description:High-throughput RNA sequencing (RNA-Seq) has enabled accurate gene discovery and expression estimation, but robust differential analysis of gene and transcript abundances has proven difficult. We present a new algorithm, implemented in the freely available tool Cuffdiff, which integrates transcript-level expression estimation with a method to control for variability across replicate samples. Cuffdiff robustly identifies differentially regulated isoforms and genes and reveals differential splicing or promoter-preference changes. We demonstrate the accuracy of our approach through differential analysis of lung fibroblasts in response to loss of the developmental transcription factor HOXA1 and uncover a critical role for this gene in the maintenance of adult cells. We show that HOXA1 is required for lung fibroblast and HeLa cell cycle progression, and loss of HOXA1 results in significant expression level changes in thousands of individual transcripts, along with isoform switching events in key regulators of the cell cycle. Lung Fibroblasts were transfected with either a HOXA1 directed siRNA pool or a scramble non-targeting siRNA control. RNA was collected 48 hours after transfection and changes in gene expression were assayed for using Agilent microarrays.
2012-12-11 | E-GEOD-37690 | biostudies-arrayexpress
Project description:Lung cancer is the single most frequent cause of cancer death worldwide and is relatively more common in males. For reasons that are currently unknown, lung cancer is also associated with significantly worse outcomes in men than women. Here we examine the pulmonary transcriptome in lung cancer at a systems level through network analysis. We compare gene expression networks in affected and unaffected tissue derived from 126 patients with lung cancer. Examination of tissue-specific co-expression patterns reveals markedly poor preservation of a sex-associated gene co-expression network in tumor tissue.
2021-06-15 | GSE151101 | GEO
Project description:A defining feature of idiopathic pulmonary fibrosis is the regional heterogeneity of the lung pathology. Here we established methodology to study the transcriptome of spatially discrete morphological areas in IPF lung tissue through the integration of laser capture microdissection of formalin fixed paraffin embedded lung tissue with low input RNA-Seq. We applied this methodology to obtain an in situ transcriptome for fibroblast foci and alveolar septae from IPF tissue as well as alveolar septae from age sex-matched control lung tissue. Differential gene expression analysis was performed between IPF alveolar septae vs control alveolar septae and between IPF fibroblast foci vs alveolar epithelium. Metacore TM was used for gene enrichment analysis of significantly differentially expressed genes, for transcription factor (TF) network analysis to identify predicted TF from human TF-target gene interaction.
2022-03-02 | GSE169500 | GEO