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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Multi-omics analysis of primary glioblastoma cell-lines shows recapitulation of pivotal molecular features of parental tumors

ABSTRACT: The goal of the study was to describe and compare the genomic landscape of Glioblastoma parental tumors and PAIRED patient derived cell lines(PDCLs). This approach enables to examine and estimate the extent to which PDCLs recapitulates the genome landscape of parental tumors - which is important for experimental model validation. In addition the consistent differences between tumors and PDCL can be evaluated in order to identify the model's weak points. In the enclosed data set, copy number variation analysis for 10 pairs of Glioblastoma tumors and their paired PDCLs are given(20 samples). Complementary data on transcriptome have been deposited at ArrayExpress under accession number E-MTAB-4803 (http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-4803).

ORGANISM(S): Homo sapiens

SUBMITTER: Shai Rosenberg

PROVIDER: E-MTAB-4804 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Multi-omics analysis of primary glioblastoma cell-lines shows recapitulation of pivotal molecular features of parental tumors

Project description:The goal of the study was to describe and compare the genomic landscape of Glioblastoma parental tumors and PAIRED patient derived cell lines(PDCLs). This approach enables to examine and estimate the extent to which PDCLs recapitulates the genome landscape of parental tumors - which is important for experimental model validation. In addition the consistent differences between tumors and PDCL can be evaluated in order to identify the model's weak points. In the enclosed experiment, nine pairs of Glioblastoma tumors and paired PDCL (18 samples) were analyzed for transcriptome. Complementary data on copy-number variation have been deposited at ArrayExpress under accession number E-MTAB-4804 (http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-4804).

2016-11-01 | E-MTAB-4803 | biostudies-arrayexpress

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Project description:The Galectin-7 gene has been found subregulated in several cervical cancer cell lines and in clinical samples. To study how the ectopic expression of Galectin-7 affect the microenvironment of the tumor, we used microarrays to analyze transcriptome of HeLa and SiHa tumors. Cells were transfected with a viral vector with the Galectin-7 gene and negative controls, the cells were injected in nude mouse. The tumor was recuperated and analyzed in mouse microarrays in 3 biological replicates, to study gene expression changes. Array data from the same study has also been deposited at ArrayExpress under accession number E-MTAB-3306 (https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-3306/) and E-MTAB-3307 (https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-3307/)

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Project description:Transgenerational effects of early experience on behavioural, hormonal and gene expression responses to acute stress in the precocial chicken. The present accession presents the data from the adult chicken of the first (parental) generation.To access data for the young chicken of the first (parental) generation see accession E-MTAB-924. The male offspring of the birds of the first (parental) generation is also available in ArrayExpress with accession E-MTAB-925.

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RNA-seq of human whole-blood samples before and after the administration of recombinant human erythropoietin

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Project description:Genome-wide methylation profiles were generated as part of a multi-omics characterization (SNP array, WES, RNA-seq, cDNA microarray) of a panel of gliomasphere cell lines and matched parental tumors. See https://www.ncbi.nlm.nih.gov/pubmed/27571888 about the GlioTeX panel. Methylation profiling data in this record come from tumour samples. SNP array (ArrayExpress E-MTAB-4804), cDNA microarray (ArrayExpress E-MTAB-4803), WES and RNAseq (European Genome-Phenome Archive EGAS00001001871) have been published before. In addition, for the current project we compare 450K methylation data to nanopore sequencing based methylation profiles. These sequencing data will be accessible via European Genome-Phenome Archive (EGAS00001002213). Please also refer to https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-5795/files/E-MTAB05795.additional.1.zip for further information on the background of this multi-omics study.

2017-06-24 | E-MTAB-5797 | biostudies-arrayexpress

Transgenerational early stress affymetrix gene expression male offspring chicken

Project description:Transgenerational effects of early experience on behavioural, hormonal and gene expression responses to acute stress in the precocial chicken. The data for the parental stressed and control birds is available in ArrayExpress with accession E-MTAB-924, while this experiment only concerns their offspring that never been exposed to early life stress.

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