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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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P19 neuronal cell differentiation

ABSTRACT: We comprehensively investigated the neural-splicing using P19 cells, set up nine filtering conditions, and obtained 262 candidate exons (236 genes). Results of semi-quantitative RT-PCR in randomly selected 30 candidates suggested that 87% of the candidates were actually changed more than double compared with the undifferentiated and differentiated cells. GO analysis and pathway analysis also showed that these 236 candidate genes were highly involved in the neural events. These results suggested that our extraction of alternative exons was quite reasonable and successful. We have biological duplicates in this project. We essentially compared Day 7 (neural-differentiated) against Day0 (Undifferentiated)

ORGANISM(S): Mus musculus

SUBMITTER: Hitoshi Suzuki

PROVIDER: E-GEOD-23710 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Comprehensive analysis of alternative splicing and functionality in neuronal differentiation of P19 cells.

Suzuki Hitoshi H Osaki Ken K Sano Kaori K Alam A H M Khurshid AH Nakamura Yuichiro Y Ishigaki Yasuhito Y Kawahara Kozo K Tsukahara Toshifumi T

PloS one 20110218 2

<h4>Background</h4>Alternative splicing, which produces multiple mRNAs from a single gene, occurs in most human genes and contributes to protein diversity. Many alternative isoforms are expressed in a spatio-temporal manner, and function in diverse processes, including in the neural system.<h4>Methodology/principal findings</h4>The purpose of the present study was to comprehensively investigate neural-splicing using P19 cells. GeneChip Exon Array analysis was performed using total RNAs purified ...[more]

PMID: 21365003

Similar Datasets

P19 neuronal cell differentiation

Project description:We comprehensively investigated the neural-splicing using P19 cells, set up nine filtering conditions, and obtained 262 candidate exons (236 genes). Results of semi-quantitative RT-PCR in randomly selected 30 candidates suggested that 87% of the candidates were actually changed more than double compared with the undifferentiated and differentiated cells. GO analysis and pathway analysis also showed that these 236 candidate genes were highly involved in the neural events. These results suggested that our extraction of alternative exons was quite reasonable and successful.

2011-03-10 | GSE23710 | GEO

Effects of PMA on exon usage of HL60, THP-1, and U937 cells

Project description:Myeloid leukemia cell lines HL60, THP-1, and U937 undergo macrophage-like differentiation after treatment with phorbol ester. To explore genes whose exon usage was altered during macrophage differentiation, we compared exome of PMA-treated (differentated) and vehicle-treated (undifferentiated) myeloid cell lines. HL60, THP-1, and U937 cells were treated with either phorbol 12-myristate 13-acetate (PMA,30nM) or its vehicle (DMSO) for 3 days, and subjected to exome analysis using Affymetrix human exon 1.0ST arrays.

2013-09-25 | E-GEOD-20567 | biostudies-arrayexpress

A novel class of alternative 3M-bM-^@M-^Y-terminal exons is involved in cell-cycle regulation by topoisomerase inhibitors

Project description:Alternative 3M-bM-^@M-^Y-terminal exons, which use intronic polyadenylation sites, are generally unconserved and lowly expressed, while the main gene products end in the last exon of genes. In this study, we discover a class of human genes, where the last exon appeared recently during evolution, and the major gene product uses an alternative 3M-bM-^@M-^Y-terminal exon corresponding to the ancestral last exon of the gene. This novel class of alternative 3M-bM-^@M-^Y-terminal exons are down-regulated on a large scale by doxorubicin, a cytostatic drug targeting topoisomerase II, and play a role in cell cycle regulation, including centromere-kinetochore assembly. The RNA-binding protein, HuR/ELAVL1 is a major regulator of this specific set of alternative 3M-bM-^@M-^Y-terminal exons. HuR binding to the alternative 3M-bM-^@M-^Y-terminal exon in the pre-messenger RNA promotes its splicing, and is reduced by topoisomerase inhibitors. These findings provide new insights into the evolution, function and molecular regulation of alternative 3M-bM-^@M-^Y-terminal exons. 6 samples of MCF7 cells exposed to different treatments were analyzed: 3 x control_6 hours; 3 x doxorubicin_6 hours.

2014-02-04 | E-GEOD-53474 | biostudies-arrayexpress

Exon array analysis for SFEBq differentiation-defective clones and good clones

Project description:It remains controversial whether human induced pluripotent stem cells (hiPSCs) are distinct from human embryonic stem cells (hESCs) in their molecular signatures and differentiation properties. We examined the gene expression and DNA methylation of 49 hiPSC and 10 hESC lines and identified no molecular signatures that distinguished hiPSCs from hESCs. Comparisons of the in vitro directed neural differentiation of 40 hiPSC and four hESC lines showed that most hiPSC clones were comparable to hESCs. However, in seven hiPSC clones, significant amount of undifferentiated cells persisted even after neural differentiation and resulted in teratoma formation when transplantated into mouse brains. These differentiation-defective hiPSC clones were marked by higher expression of several genes, including those expressed from long terminal repeats of human endogenous retroviruses. These data demonstrated that many hiPSC clones are indistinguishable from hESCs, while some defective hiPSC clones need to be eliminated prior to their application for regenerative medicine. We extracted total RNA from 3 differentiation-defective clones, 3 good clones and 2 somatic cells, and hybridized them to Affymetrix exon arrays.

2013-12-03 | E-GEOD-42449 | biostudies-arrayexpress

Analysis of liver RNA from SRSF3 hepatocyte knockout mice versus wild-type littermates

Project description:Livers from three SRSF3HKO mice and 3 wild-tyope littermates were used to analyze changes in exon utilization and gene expression. two genotypes, three replicates each

2012-12-01 | E-GEOD-35686 | biostudies-arrayexpress

Exon Level Expression Profiling: Induced adult neurogenesis in the olfactory epithelium

Project description:Transcriptome analysis of RNA samples from mice olfactory epithelium Gene expression profiling in the olfactory epithelium was performed to obtain a better understanding of the processes mediating cell replacement. We analyzed epitheliual tissue from 3 adult male mice at 5 days following ipsilateral olfactory bulbectomy (OBX). Total RNA was isolated and anlayzed using the Affymetrix Mouse Exon 1.0 ST platform. Array data was processed by Affymetrix Exon Array Computational Tool.

2013-04-11 | E-GEOD-45931 | biostudies-arrayexpress

Gene expression profiles of control and EWS-FLI1-transduced neural crest stem cells

Project description:Expression profiles were generated from hESC-derived neural crest stem cells following transduction with GFP control vector or EWS-FLI1 vector. Expression was analyzed in stem cell conditions 5 days after transduction (undifferentiated conditions) and after 6 weeks in differentiation media (differentiation conditions). Changes in gene expression over time were compared between control and EWS-FLI1 expresssing cells. Total RNA was extracted from 3 replicates for each of 4 conditions (undifferentiated control, undifferentiated EWS-FLI1, differentiated control and differentiated EWS-FLI1. Samples were analyzed by Affymetrix exon arrays using standard procedures.

2015-05-15 | E-GEOD-68898 | biostudies-arrayexpress

Identification of Cottontail rabbit papillomavirus E2 protein regulated genes

Project description:Transcriptome analyses of RNA from C33a cells after induction of CRPV E2 expression by doxycycline C33a cells were established that carry the doxycycline-inducible pRTS-CRPV E2 vector. We analyzed 3 biological replicates (induced/uninduced) using the Affymetrix Human Exon 1.0 ST platform.

2015-03-28 | E-GEOD-67345 | biostudies-arrayexpress

Genome-wide analysis of differentially expressed genes and splicing isoforms in clear cell Renal Cell Carcinoma

Project description:In this study we performed a genome wide analysis of the entire complement of mRNAs in clear cell renal cell carcinomas (ccRCC) by means of the Affymetrix Exon Array platform. The analyses were performed both at gene and exon level. Under our parameters over 2,000 genes resulted differentially expressed, and about 250 genes resulted alternative spliced showing differential inclusion of specific cassette exons comparing tumor and non tumoral tissues. 20 total samples were used for exon array analysis: 10 ccRCC tumor sample (T) and their matched non-tumor (NT) kidney tissues samples. All exon array data were analyzed using Partek Genomic Suite 6.4 software (Partek). The robust multi-array average (RMA) algorithm was used for the gene- and exon-level intensity analyses. Data were M-oM-,M-^Altered to consider only those probe sets included in the M-bM-^@M-^\Core Meta-ProbesetM-bM-^@M-^]. Lists of genes and exons with significant variation of the expression levels were generated by using a 0.01 FDR criterion as a significant cutoff. Partek list of significant exon-level probesets (FDR corrected p-value < 0.01) and exon level ANOVA test list were used to create - by an ad hoc Python script - a database of significant probesets from Exon Array experiments. To make more stringent the analysis criteria we excluded from the final exon lists all those cases in which Exon Array revealed a significant change at gene-level. This database we created has been used to explore simple exon skipping events using as reference ASPicDB single exon skipping splicing events after mapping Affymetrix probesets on ASPicDB .gtf files. A single exon from the Partek list was defined significantly skipped only if its adjacent exons were not, by using 0.01 and 0.05 p-value criterions as a significant cutoff for the M-bM-^@M-^\skippedM-bM-^@M-^] and adjacent exons, respectively.

2013-09-06 | E-GEOD-47032 | biostudies-arrayexpress

Transforming pluripotency: an exon-level study of malignancy-specific transcripts in human embryonal carcinoma and embryonic stem cells

Project description:Exon-level transcriptome analysis of embryonal carcinoma (EC) and embryonic stem (ES) cell lines. To circumvent difficulties of isolating pure populations of cancer stem cells for the purpose of identifying malignancy-specific gene expression, we have compared exon-resolution transcriptomic profiles of five embryonal carcinoma (EC) cell lines, a histological subtype of germ cell tumour, to their non-malignant caricature, specifically six human embryonic stem (ES) cell lines. Both cell types are readily accessible, and were purified for undifferentiated cells only. We identified a set of 28 differentially expressed genes, many of which had cancer and stemness roles. Overexpression of the recently discovered pluripotency gene NR5A2 in malignant EC cells revealed an intriguing indication of how WNT-mediated dysregulation of pluripotency is involved with malignancy. At the exon-level, alternative splicing events were detected in ZNF195, DNMT3B and PMF1, and alternative promoters were detected for ASH2L and ETV5. These events were validated by RT-PCR-based methods in EC and ES lines, and further explored within a series of 25 primary tumours, where the alternative splicing event in the de novo DNA methyltransferase DNMT3B may have functional consequences. In conclusion, we have identified malignancy-specific gene expression differences within a rigorous pluripotent stem cell context. These findings are of particular interest for both germ cell tumour and ES cell biology, and in general to the concept of cancer stem cells. 5 EC and 6 ES cell lines gown on plastic and feeders respectively were sorted for the pluripotency marker SSEA3, then profiled on the Affymetrix Human Exon 1.0 ST platform. 3 additional EC lines grown on feeders and ES medium were also profiled in the same way. Data was analyzed using Qlucore (PCA), XRAY and limma (gene- and exon-level expression differences) and SAM (two-class pair-wise Significance of Microarrays).

2015-01-01 | E-GEOD-34855 | biostudies-arrayexpress

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