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Unknown,Transcriptomics,Genomics,Proteomics

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Liver cell lines under hyper-IL6 stimulation (mRNA)

ABSTRACT: In this study, two hepatic cell lines were stimulated with hyper-IL-6 for 6, 24, 48 and 72 h or kept untreated.

ORGANISM(S): Homo sapiens

SUBMITTER: Iris Behrmann

PROVIDER: E-MTAB-10646 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Primary healthy liver cells under hyper-IL6 stimulation (mRNA)

Project description:In this study, primary healthy liver cells obtained from patients with colon cancer and liver metastasis were stimulated with hyper-IL-6 for 6, 24, 48 and 72 h or kept untreated. Both mRNA and miRNA levels were characterized (this is mRNA dataset).

2019-02-28 | E-MTAB-6571 | biostudies-arrayexpress

Response of several cell lines originated from liver, skin and colon to stimulation by IFNg, hyper-IL6, IL27 and OSM, investigated at mRNA level

Project description:In this study 6 cell lines originated from liver, skin and colon tumours as well as 3 non-tumour cell lines from the same organs were profiled with and without stimulation by 4 cytokines: IFNg, hyper-IL6, IL27 and OSM. The main objective was investigation of downstream effects of the stimulation if these cancer cell lines as well as in healthy tissues.

2018-10-01 | E-MTAB-6080 | biostudies-arrayexpress

Primary healthy liver cells under hyper-IL6 stimulation (miRNA)

Project description:In this study, primary health liver cells obtained from patients with colon cancer and liver metastasis were stimulated with hyper-IL-6 for 6, 24, 48 and 72 h or kept untreated. Both mRNA and miRNA levels were characterized (this is miRNA dataset).

2019-02-28 | E-MTAB-6572 | biostudies-arrayexpress

Integrative analysis reveals relationships of genetic and epigenetic alterations in osteosarcoma [methylation]

Project description:Osteosarcomas are the most common primary malignant tumours of bone, and almost all conventional osteosarcomas are high-grade tumours showing complex genomic aberrations. We have integrated genome-wide genetic and epigenetic profiles from the EuroBoNeT panel of 19 human osteosarcoma cell lines based on microarray technologies. The cell lines showed complex patterns of DNA copy number changes, where copy number gains were significantly associated with gene-rich regions of the genome and losses with gene-poor areas. Integration of the datasets showed that the mRNA levels were regulated by either alterations in DNA copy number or DNA methylation. Using a recurrence threshold of 6/19 (> 30 %) cell lines, 348 genes were identified as having alterations of two data types (gain or hypo-methylation/over-expression, loss or hyper-methylation/under-expression). These genes are involved in embryonic skeletal system development and morphogenesis, as well as remodelling of extracellular matrix. Several genes were hyper-methylated and under-expressed compared to normal osteoblasts, and expression could be reactivated by demethylation using 5-Aza-2M-bM-^@M-^Y-deoxycytidine treatment for all four genes tested. Globally, there was as expected a significant positive association between gain and over-expression, loss and under-expression as well as hyper-methylation and under-expression, but gain was also associated with hyper-methylation and under-expression, suggesting that hyper-methylation may oppose the effects of increased copy number for some genes. Integrative analysis of genome-wide genetic and epigenetic alterations identified mechanistic dependencies and relationships between DNA copy number and DNA methylation in terms of regulating mRNA expression levels in osteosarcomas, contributing to better understanding of osteosarcoma biology. Comparison of DNA methylation patterns in 19 osteosarcoma cell lines and 6 normal samples (osteoblasts and bones)

2012-12-06 | E-GEOD-36002 | biostudies-arrayexpress

Integrative analysis reveals relationships of genetic and epigenetic alterations in osteosarcoma.

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2012-12-06 | E-GEOD-36004 | biostudies-arrayexpress

Characterisation of nuclear architectural alterations during in vitro differentiation of human stem cells of myogenic origin

Project description:Cell differentiation is based on a synchronised orchestra of complex pathways of intrinsic and extrinsic signals that manifest in the induced expression of specific transcription factors and pivotal genes within the nucleus. One cannot ignore the epigenetic status of differentiating cells, comprising not only histones and DNA modifications but also the spatial and temporal intranuclear chromatin organisation, which is an important regulator of nuclear processes. In the present study, we investigated the nuclear architecture of human primary myoblasts and myocytes in an in vitro culture, with reference to global changes in genomic expression. Repositioning of the chromosomal centromeres, along with alterations in the nuclear shape and volume, was observed as a consequence of myotube formation. Moreover, the microarray data showed that during in vitro myogenesis cells tend to silence rather than induce gene expression. The creation of a chromosome map marked with gene expression changes that were at least 2-fold confirmed the observation. Additionally, almost all of the chromosomal centromeres in the differentiated cells preferentially localised near the nuclear periphery when compared to the undifferentiated cells. The exceptions were chromosomes 7 and 11, in which we were unable to confirm the centromere repositioning. In our opinion, this is the first reported observation of the movement of chromosomal centromeres along differentiating myogenic cells. Based on these data we can conclude that the myogenic differentiation with global gene expression changes is accompanied by the spatial repositioning of chromosomes and chromatin remodelling, which are important processes that regulate cell differentiation. Six samples from human skeletal muscle stem cells populations before and after differentiation were analysed

2013-04-06 | E-GEOD-45819 | biostudies-arrayexpress

Gene Expression profile of Breast Cancer Stem Cell-like HMLE_sh_ECad cells after treatment with DMSO or CID49843203

Project description:Breast Cancer stem cell-like line, HMLEshECad, and isogenic control line, HMLEshGFP, were treated with DMSO or with Breast Cancer Stem Cell-like Cell selective compound CID49843203

2011-11-15 | E-MTAB-884 | biostudies-arrayexpress

Transcription profiling of human bone tumours to evaluate four commercial high-resolution oligonucleotide microarray platforms.

Project description:Evaluation of four commercial high-resolution oligonucleotide microarray platforms, Affymetrix Genome-Wide Human SNP Array 6.0, Agilent Human Genome CGH 244A, Illumina HumanExon510s-duo and Nimblegen HG18 CGH 385k WG tiling v1.0, for genomic profiling of bone tumours.

2010-07-01 | E-TABM-805 | biostudies-arrayexpress

Identification of the differences between gene expression in normal human dermal fibroblasts (NHDF cell line) infected with Borrelia burgdorferi sensu lato spirochetes

Project description:The similarity of Lyme borreliosis to other diseases and the complex pathogenesis cause diagnostic and therapeutic difficulties. Changes at the cellular and molecular level after Borrelia sp. infection remain still poorly understood. Therefore, the present study focused on the gene expression in human dermal fibroblasts in differentiation of infection with Borrelia garinii, Borrelia afzelii and Borrelia burgdorferi sensu stricto spirochetes. For microarray analysis 10 samples were used: 3 control samples - K, 2 samples of NHDF cells infected with Borrelia garinii - G, 2 samples of NHDF cells infected with Borrelia afzelii - A and 3 samples of NHDF cells infected with Borrelia burgdorferi sensu stricto - SS.

2015-05-12 | E-GEOD-68741 | biostudies-arrayexpress

The HDAC inhibitor Givinostat modulates key hematopoietic genes in JAK2V617F cells, affecting proliferation, differentiation and apoptosis

Project description:We investigated the mechanism of action of the HDAC inhibitor Givinostat in JAK2V617F cells. We confirm that the drug inhibits colony formation and proliferation and induces apoptosis at doses 2-3 fold lower in JAK2V617F (HEL, UKE1 and SET2) compared to JAK2 wild type cell lines (K562, KU812, THP1 and KG1). By global gene expression analysis, we observed 293 common genes in HEL and UKE1 modulated at 6 hour by Givinostat (179 up and 114 down), of which 8/8 were validated by RTQ-PCR. 25, 28 and 33 modulated genes are implicated in the regulation of proliferation, apoptosis and hematopoiesis, respectively. Interestingly, 9 genes, known to be deregulated in MPN (myeloproliferative neoplasms) patients cells, were normalized by Givinostat. The hematopoietic transcription factors NFE2 and C-MYB were downmodulated by the drug specifically in JAK2V617F cells, and ETS1 was upregulated in all cell lines, at both the RNA and protein levels. Modulation of NFE2 and C-MYB was JAK2 dependent, as shown by use of the JAK2 inhibitor AG490. Finally, we suggest that the inhibition of NFE2 and induction of ETS1, also observed in freshly isolated CD34+ cells from MPN patients, may be at least in part responsible for the observed inhibition of erythroid differentiation by the drug. Gene expression profiling, JAK2V617F cell lines, ITF2357. This series of microarray experiments contains the gene expression profiles of independent triplicates of HEL and UKE1 erythroleukemia cell lines bearing the JAK2V617F mutation, before and after ITF2357 treatment. 100 nanograms of total RNA were processed, and fragmented biotin-labelled single-stranded DNA target was hybridized to the GeneChipÂ® Gene 1.0 ST array following the Affymetrix manufacturer's instructions.

2012-07-16 | E-GEOD-27615 | biostudies-arrayexpress

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