Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

25 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcription profiling of human embryonic stem cell line containining HSR H14, and parent H14 l

ABSTRACT: Homogenous staining regions (hsr) are cytogenetic representations of a gene amplification. They are found exclusively in tumour cells. We found a hsr in the human embryonic stem cell (hESC) line H14, this is the first report of a hsr in hESCs. FISH and CGH studies showed that the hsr was derived from chromosome 17p11.2. The gene expression analysis studies were performed to identify the genes upregulated due to the hsr by comparison the the hsr-contianing H14 cells with a karyotypically normal parent H14 cell line. Experiment Overall Design: H14 HSR positive embryonic stem cells and H14 HSR negative cells were hybridised to Affymetrix U133 Plus 2.0 expression arrays. Replicates were also run using H14 positive and H14 negative cells from different passages.

ORGANISM(S): Homo sapiens

SUBMITTER: Duncan Baker

PROVIDER: E-GEOD-6561 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Adaptation to culture of human embryonic stem cells and oncogenesis in vivo.

Baker Duncan E C DE Harrison Neil J NJ Maltby Edna E Smith Kath K Moore Harry D HD Shaw Pamela J PJ Heath Paul R PR Holden Hazel H Andrews Peter W PW

Nature biotechnology 20070201 2

The application of human embryonic stem cells (HESCs) to provide differentiated cells for regenerative medicine will require the continuous maintenance of the undifferentiated stem cells for long periods in culture. However, chromosomal stability during extended passaging cannot be guaranteed, as recent cytogenetic studies of HESCs have shown karyotypic aberrations. The observed karyotypic aberrations probably reflect the progressive adaptation of self-renewing cells to their culture conditions. ...[more]

PMID: 17287758

Similar Datasets

Expression data from hsr containing human embryonic stem cell line, H14, and parent H14 human embryonic stem cell line.

Project description:Homogenous staining regions (hsr) are cytogenetic representations of a gene amplification. They are found exclusively in tumour cells. We found a hsr in the human embryonic stem cell (hESC) line H14, this is the first report of a hsr in hESCs. FISH and CGH studies showed that the hsr was derived from chromosome 17p11.2. The gene expression analysis studies were performed to identify the genes upregulated due to the hsr by comparison the the hsr-contianing H14 cells with a karyotypically normal parent H14 cell line. Keywords: karyotypically abnormal hESC vs karyotypically normal hESC.

2007-02-10 | GSE6561 | GEO

Project description:Hob6 positive and negative cells

| PRJNA193190 | ENA

Homo sapiens

Project description:Expression data from hsr containing human embryonic stem cell line, H14, and parent H14 human embryonic stem cell line.

| PRJNA98779 | ENA

Hippocampal cells multiplex positive and negative engrams

Project description:Hippocampal cells multiplex positive and negative engrams

| PRJNA816561 | ENA

Expression data from +7 hNPCs and diploid hNPCs

Project description:Human Neural progenitor cells have been found to have karyotypic abnormalities. In this study we explored the gene changes between hNPCs that are karyotypically normal and hNPCs with a trisomy of chromosome 7. We used Affymetrix GeneChips to study gene expression changes between karyotypically normal hNPCs and trisomy 7 hNPCs.

2009-10-01 | GSE18349 | GEO

Effect of MOK in LPS-induced responses in microglial cells

Project description:To investigate the possible impact of MOK in microglial immune responses, we tested the effect of LPS treatment in MOK-KO (H14) vs. WT SIM-A9 cells.

2023-06-30 | GSE234160 | GEO

Transcriptional responses of cancer cells to heat shock-inducing stimuli involve amplification of robust HSF1 binding

Project description:Background. The Heat Shock Response (HSR) is an evolutionarily conserved mechanism that helps cells adapt to environmental stresses. Heat Shock Factor 1 (HSF1) is a master HSR transcription factor that is long known to bind at promoters of its target HSP genes to rapidly activate their transcription. However, recent genome-wide studies revealed HSF1 binding at thousands of sites outside of heat-shock responsive gene promoters, implying a broader role of HSF1 in HSR. Results. We asked how the widespread HSF1 binding is established and to what extent it may be related to transcription activation. To answer these questions, we examined responses of two different human cancer cell lines to two stimuli that induce HSR, exposure to 42C and inorganic arsenic at the ambient temperature, by manually integrating ChIP-sequencing against HSF1, RNA Pol II, H3K4Me3 with nascent RNA- and ATAC-sequencing datasets in cells before and during HSR induced by these two stimuli. We show that widespread HSF1 binding is a temperature-agnostic hallmark of HSR whose genome-wide patterns combine cell type specificity with robustness to the nature of a stimulus and magnitude of activation. Mechanistically, HSR involves amplification of pre-existing low level HSF1 binding with few changes in accessible chromatin. HSF1 binding patterns show more stability than transcriptionally activated genes both between conditions and between cell lines. Conclusions. Comparing responses of distant cell lines to two HSR-inducing stimuli allowed us to define several features of HSR. Genome-wide HSF1 binding is a sensitive readout of HSR whose genome-wide patterns retain cell type identity across a broad dynamic range. The pre-existing genomic architecture is retained during HSR down to individual loci. Context-specific transcription involving common HSF1 binding favors a model of regulation by combinatory interplay of rigid transcription factor patterns.

2023-10-30 | GSE209685 | GEO

Transcriptional responses of cancer cells to heat shock-inducing stimuli involve amplification of robust HSF1 binding

2023-10-30 | GSE209675 | GEO

Transcriptional responses of cancer cells to heat shock-inducing stimuli involve amplification of robust HSF1 binding

2023-10-30 | GSE209667 | GEO

Evaluation of Integrin aE-positive and negative cells

Project description:Evaluation of Integrin aE-positive and negative cells

| PRJNA638956 | ENA