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GSE24783
Homo sapiens
5 Downloadable Samples
Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Hyperthermia is widely used to treat patients with various cancers. The 42.5C is well known as inflection point of hyperthermia and generally up to 42C of hyperthermia is used in clinical case to combine with other therapy. Here, the effects of heat stress at 42 or 44C for 90 min on the gene expression in HSC-3 human oral squamous carcinoma cells were investigated using an Affymetrix GeneChip system. The cells were treated with heat stress (42 or 44C for 90 min) and followed by incubation for 0, 6, or 12 h at 37C. The percentage of cell death was 5.0 1.5 (mean SD) at 42C for 12 h and 17.4 0.6 at 44C for 12 h. Of approximately 47,000 probe sets analyzed, many genes that were differentially expressed by a factor 2.0 or greater were identified in the cells treated with heat stress at 42 and 44C.
Publication Title
Gene networks related to the cell death elicited by hyperthermia in human oral squamous cell carcinoma HSC-3 cells.
Sample Metadata Fields
Cell line, Treatment, Time
View Samples- Homo sapiens
- 9 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Hyperthermia is widely used to treat patients with various cancers. 42.5C is well known as the inflection point of hyperthermia and generally up to 42C of hyperthermia is used in clinical cases combined with other therapies. Here, the effects of heat stress at 42 or 44C for 15 min on the gene expression in human lymphoma U937 cells were investigated using an Affymetrix GeneChip system. The cells were treated with heat stress (42 or 44C for 15 min), followed by incubation for 0, 1, 3 or 6 h at 37C. The percentage of DNA fragmentation was 8.4 2.2 (mean SD) at 42C for 6 h and 21.0 2.0 at 44C for 6 h. Of approximately 47,000 probe sets analyzed, many genes that were differentially expressed by a factor 2.0 or greater were identified in the cells treated with heat stress at 42 and 44C.
Publication Title
Identification of biological functions and gene networks regulated by heat stress in U937 human lymphoma cells.
Sample Metadata Fields
Specimen part, Cell line, Treatment
View Samples- Homo sapiens
- 5 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Hyperthermia (41C <) is widely used to treat patients with various cancers. Here, the effects of hyperthermia (42C for 90 min) on the gene expression in human lymphoma U937 cells were investigated using an Affymetrix GeneChip system. The cells were treated with hyperthermia (42C for 90 min) and followed by incubation for 0, 1, 3 or 6 h at 37C. The percentage of DNA fragmentation was 7.5 0.9 (mean SD), 10.1 0.2, and 17.3 2.3 at the incubation periods of 1, 3, and 6 h, respectively. Of approximately 47,000 probe sets analyzed, the hyperthermia down-regulated 4,214 probe sets and up-regulated 1,334 by a factor 2.0 or greater.
Publication Title
Gene networks involved in apoptosis induced by hyperthermia in human lymphoma U937 cells.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 3 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Hyperthermia is widely used to treat patients with various cancers. Here, the effects of heat stress at 41C for 30 min (mild hyperthermia) on the gene expression in OUMS-36 human normal fibroblast cells were investigated using an Affymetrix GeneChip system. The cells were treated with mild hyperthermia, followed by incubation for 0, 1, or 3 h at 37C. No cell death was observed in the mild hyperthermia-treated cells. On the other hand, many genes that were differentially expressed by a factor 1.5 or greater were identified in the cells treated with the mild hyperthermia.
Publication Title
Common gene expression patterns responsive to mild temperature hyperthermia in normal human fibroblastic cells.
Sample Metadata Fields
Cell line, Treatment
View Samples- Homo sapiens
- 4 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Hyperthermia is widely used to treat patients with various cancers. Here, the effects of heat stress at 41C for 30 min (mild hyperthermia) on the gene expression in Hs68 human skin normal fibroblast cells were investigated using an Affymetrix GeneChip system. The cells were treated with mild hyperthermia, followed by incubation for 0, 1, or 3 h at 37C. No cell death was observed in the mild hyperthermia-treated cells. On the other hand, many genes that were differentially expressed by a factor 1.5 or greater were identified in the cells treated with the mild hyperthermia.
Publication Title
Common gene expression patterns responsive to mild temperature hyperthermia in normal human fibroblastic cells.
Sample Metadata Fields
Sex, Specimen part, Cell line, Treatment
View Samples- Homo sapiens
- 4 Downloadable Samples
- Affymetrix Human Genome U133A Array (hgu133a)
Description
The rationale underlying hyperthermia is the fact that temperatures over 42.5C are highly cytotoxic to tumor cells. On the other hand, although mild hyperthermia at a range from 39 to 41C alone did not induce cytotoxicity in tumor cells, mild hyperthermia is reported to show a synergism with radiotherapy and anti-cancer drugs. Here, the effects of mild hyperthermia (41C for 30 min) on the gene expression in human lymphoma U937 cells were investigated using by an Affymetrix GeneChip system. Although the cells treated with the mild hyperthermia did not induce apoptosis, a significant increase in protein levels of heat shock proteins, Hsp40 and Hsp70, was observed following activation of heat shock factor-1. At 3 h post-treatment, 938 probe sets that were differentially expressed by >1.5-fold were identified.
Publication Title
Genes and genetic networks responsive to mild hyperthermia in human lymphoma U937 cells.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 4 Downloadable Samples
- Affymetrix Human Genome U133A Array (hgu133a)
Description
Paeoniflorin (PF) isolated from paeony root (Paeoniae radix) has been used as an herbal medicine in East Asis for its anti-allergic, anti-inflammatory, and immunoregulatory effects. PF is known to be a chemical heat shock protein (HSP) inducer. The effects on the gene expression in human lymphoma U937 cells treated with PF were investigated using by an Affymetrix GeneChip system. PF treatment induced Hsp70 expression in U937 cells in a dose- and time-dependent manner as shown in Western blot analysis. When the cells were treated with PF (160 g/ml; 30 min), 41 up-regulated and 23 down-regulated genes were identified.
Publication Title
Identification of genes responsive to paeoniflorin, a heat shock protein-inducing compound, in human leukemia U937 cells.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 5 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
In the developing brain, neural progenitor cells (NPCs) switch the differentiation competency via changing gene expression profiles that are governed partly by epigenetic control such as histone modification, although the precise mechanism is unknown. Here we found that ESET/Setdb1/KMT1E, a histone H3 Lys-9 (H3K9) methyltransferase, was highly expressed at early stages of brain development but down-regulated over time, and that ablation of ESET led to decreased H3K9 trimethylation and misregulation of genes, resulting in severe brain defects and early lethality. In the mutant brain, endogenous retrotransposons were derepressed, and non-neural gene expression was activated. Furthermore, early neurogenesis was most severely impaired, while astrocyte formation was enhanced. We conclude that there is an epigenetic role of ESET in temporal and tissue-specific gene regulation in the developing brain.
Publication Title
Essential roles of the histone methyltransferase ESET in the epigenetic control of neural progenitor cells during development.
Sample Metadata Fields
Sex, Specimen part
View Samples- Zea mays
- 4 Downloadable Samples
Illumina Genome Analyzer
Description
Transposable elements (TEs) comprise a substantial portion of many eukaryotic genomes and are typically transcriptionally silenced. RNA–dependent RNA polymerase 2 (RDR2) is a component of the RNA–directed DNA methylation (RdDM) silencing pathway. In maize, loss of mediator of paramutation1 (mop1) encoded RDR2 function results in reactivation of transcriptionally silenced Mu transposons and a substantial reduction in the accumulation of 24 nt short-interfering RNAs (siRNAs) that recruit RNA silencing components. An RNA–seq experiment conducted on shoot apical meristems (SAMs) revealed that, as expected based on a model in which RDR2 generates 24 nt siRNAs that suppress expression, most differentially expressed DNA TEs (78%) were up-regulated in the mop1 mutant. In contrast, most differentially expressed retrotransposons (68%) were down-regulated. This striking difference suggests that distinct silencing mechanisms are applied to different silencing templates. In addition, 6,000 genes (24% of analyzed genes), including nearly 80% (286/361) of genes in chromatin modification pathways, were differentially expressed. Overall, two-thirds of differentially regulated genes were down-regulated in the mop1 mutant. This finding suggests that RDR2 plays a significant role in regulating the expression of not only transposons, but also of genes. A re-analysis of existing small RNA data identified both RDR2–sensitive and RDR2–resistant species of 24 nt siRNAs that we hypothesize may at least partially explain the complex changes in the expression of genes and transposons observed in the mop1 mutant. Overall design: Single sequencing library was constructed for mop1 mutant and non-mutant. Each library was sequenced using 2 lanes on a Solexa flow cell. Processed data file 'ZmB73_4a.53_filtered_genes.fasta' and its README file are linked below as supplementary files. The fasta file contains the gene model ID and corresponding sequence generated from maize genome project. This fasta file was used for the following samples: GSM418173, GSM418174, GSM420173, GSM420174, GSM422828, GSM422829.
Publication Title
Loss of RNA-dependent RNA polymerase 2 (RDR2) function causes widespread and unexpected changes in the expression of transposons, genes, and 24-nt small RNAs.
Sample Metadata Fields
Age, Subject
View Samples- Homo sapiens
- 4 Downloadable Samples
- Illumina HumanHT-12 V4.0 expression beadchip
Description
A significant proportion of differentially expressed genes were associated with extracellular matrix organization and extracellular structure organization.
Publication Title
LAMA4 upregulation is associated with high liver metastasis potential and poor survival outcome of Pancreatic Cancer.
Sample Metadata Fields
Specimen part, Treatment
View Samples