Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

38 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Identification of genes that regulated by IRF4 in human cutaneous T cell lymphoma HuT-102 cells

ABSTRACT: The microarray analysis showed an interesting up-regulation in the set of genes controlling the development of Th1, mainly IFN-gamma, and other type 1 interferon response genes including CXCL10 in IRF4 knocked-down HuT-102 cells. HuT-102 cells, a human cutaneous T cell lymphoma, were transiently transfected with siRNAs against human IRF4 or firefly luciferase. Cells were incubated for 60 h at 37 centigrade. Total RNA samples were prepared from the cells. Gene expression was analyzed by an Affymetrix GeneChipÂ® system with a Human Genome U133-plus 2.0 array for analysis of over 47,000 transcripts. Sample preparation for array hybridization was carried out as described in the manufacturerâs instructions.

ORGANISM(S): Homo sapiens

SUBMITTER: Yoshiaki Tabuchi

PROVIDER: E-GEOD-22036 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Identification of genes that are regulated by TAK1 in human cutaneous T cell lymphoma HuT-102 cells

Project description:We previously reported that human T cell lymphotropic virus 1 (HTLV-1) Tax oncoprotein constitutively activates TAK1. Here, we established Tax-positive HuT-102 cells stably downregulated TAK1 expression by short-hairpin RNA (HuT-shTAK1 cells), and investigated the physiological function of TAK1. Microarray analysis demonstrated that several interferon (IFN)-inducible genes including chemokines such as CXCL10 and CCL5 were significantly downregulated in HuT-shTAK1 cells. In contrast, Tax-mediated constitutive activation of NF-kB was intact in HuT-shTAK1 cells. IRF3, a critical transcription factor in innate immunity to viral infection, was constitutively activated in a Tax-dependent manner. Activation of IRF3 and IRF3-dependent gene expression were dependent on TAK1 and TBK1. On the other hand, IRF4, another IRF family of transcription factor overexpressed in a Tax-independent manner, negatively regulated the TAK1-dependent IRF3 transcriptional activity. Together, HTLV-1 manipulates IFN signaling by regulating both positive and negative IRFs. HuT-102 cells, a human cutaneous T cell lymphoma, were stably transfected with shRNA expression vectors against human MAP3K7 (TAK1) or firefly luciferase (Luc). The cells were maintained in media containing 0.5 mg/ml G418. For the experiment, the cells were incubated in media without G418 for 36 h at 37M-BM-0C. Total RNA samples were prepared from the cells. Gene expression was analyzed by an Affymetrix GeneChipM-BM-. system with a Human Genome U133-plus 2.0 array for analysis of over 47,000 transcripts. Sample preparation for array hybridization was carried out as described in the manufacturerM-bM-^@M-^Ys instructions. Two replicates per sample type.

2009-08-18 | E-GEOD-16219 | biostudies-arrayexpress

Identification of genes that regulated by IRF4 in human cutaneous T cell lymphoma HuT-102 cells

Project description:The microarray analysis showed an interesting up-regulation in the set of genes controlling the development of Th1, mainly IFN-gamma, and other type 1 interferon response genes including CXCL10 in IRF4 knocked-down HuT-102 cells.

2010-05-29 | GSE22036 | GEO

Transcription profiling of human leukemia U937 cells response to hyperthermia

Project description:Hyperthermia (41ËC <) is widely used to treat patients with various cancers. Here, the effects of hyperthermia (42ËC 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 (42Â°C for 90 min) and followed by incubation for 0, 1, 3 or 6 h at 37Â°C. The percentage of DNA fragmentation was 7.5 Â± 0.9 (mean Â± SD), 10.1 Â± 0.2, and 17.3 Â± 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. Experiment Overall Design: U937 cells, a human lymphoma cell line, were treated with hyperthermia (42Â°C for 90 min) and followed by incubation for 0, 1, 3 or 6 h at 37Â°C. Non-treated cells were served as control. Total RNA samples were prepared from the cells. Gene expression was analyzed by an Affymetrix GeneChipÂ® system with a Human Genome U133-plus 2.0 array for analysis of over 47,000 transcripts. Sample preparation for array hybridization was carried out as described in the manufacturerâs instructions.

2008-11-15 | E-GEOD-13503 | biostudies-arrayexpress

Effects of shikonin on the gene expression of human lymphoma U937 cells

Project description:Shikonin is a active component isolated from the roots of the traditional Chinese herb Lithospermum erythrorhizon and exhibits multiple pharmacological properties, such as anti-oxidant, anti-inflammatory, and anti-tumor effects. Here, the effects of shikonin on the gene expression of human lymphoma U937 cells were investigated using an Affymetrix GeneChip system. The cells were treated with 100 nM shikonin, and followed by incubation for 3h at 37Â°C. Flow cytometry analysis with Annexin-V and propidium iodide demonstrated that no cell death was observed in the cells at 100 nM shikonin. 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 the compound. U937 cells, a human lymphoma cell line, were treated with 100 nM shikonin and followed by incubation for 3h at 37Â°C. The cells treated with dimethyl sulfoxide were served as control. Total RNA samples were prepared from the cells. Gene expression was analyzed by an Affymetrix GeneChipÂ® system with a Human Genome U133-plus 2.0 array for analysis of over 47,000 transcripts. Sample preparation for array hybridization was carried out as described in the manufacturerâs instructions.

2010-10-20 | E-GEOD-24743 | biostudies-arrayexpress

Gene profiling of the cell death induced by heat stress in HSC-3 human oral squamous carcinoma cells

Project description:Hyperthermia is widely used to treat patients with various cancers. The 42.5ËC is well known as inflection point of hyperthermia and generally up to 42ËC of hyperthermia is used in clinical case to combine with other therapy. Here, the effects of heat stress at 42 or 44ËC 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 44Â°C for 90 min) and followed by incubation for 0, 6, or 12 h at 37Â°C. The percentage of cell death was 5.0 Â± 1.5 (mean Â± SD) at 42Â°C for 12 h and 17.4 Â± 0.6 at 44Â°C 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 44Â°C. HSC-3 human oral squamous carcinoma cells were treated with heat stress (42 or 44Â°C for 90 min) and followed by incubation for 0, 6, or 12 h at 37Â°C. Non-treated cells were served as control. Total RNA samples were prepared from the cells. Gene expression was analyzed by an Affymetrix GeneChipÂ® system with a Human Genome U133-plus 2.0 array for analysis of over 47,000 transcripts. Sample preparation for array hybridization was carried out as described in the manufacturerâs instructions.

2010-10-20 | E-GEOD-24783 | biostudies-arrayexpress

Transcription profiling of human leukemia U937 cells treated with the combination of Sonazoid and ultrasound

Project description:Echo-contrast agents enhance the echogenicity of ultrasound and have been clinically used for diagonosis in current medical fields. Here, the combined effects of Sonazoid, an echo-contrast agent, and ultrasound on the gene expression in human lymphoma U937 cells were investigated using an Affymetrix GeneChip system. The cells were treated with Sonazoid (0.05%; Sonazoid only), ultrasound (0.3 W/cm2 for 1 min; ultrasound only) and the combination of Sonazoid and ultrasound (0.05% Sonazoid plus ultrasound 0.3 W/cm2 for 1 min; Sonazoid + Ultrasound) and followed by incubation for 3 h at 37Â°C. The percentage of DNA fragmentation 6 h after treatment was 5.8 Â± 1.0 (mean Â± SD, n = 3), 6.0 Â± 0.4, 13.5 Â± 1.0, and 18.3 Â± 2.3 in cells treated with control, Sonazoid only, ultrasound only and Sonazoid + Ultrasound, respectively. Of approximately 47,000 probe sets analyzed, probe sets that were differentially expressed by a factor 2.0 or greater were 40, 184 and 144 in cells treated with Sonazoid only, ultrasound only and Sonazoid + Ultrasound, respectively. Experiment Overall Design: U937 cells, a human lymphoma cell line, were treated with Sonazoid (0.05%), ultrasound (0.3 W/cm2 for 1 min) and the combination of Sonazoid and ultrasound (0.05% Sonazoid plus ultrasound 0.3 W/cm2 for 1 min) and followed by incubation for 3 h at 37Â°C. Non-treated cells were served as control. Total RNA samples were prepared from the cells. Gene expression was analyzed by an Affymetrix GeneChipÂ® system with a Human Genome U133-plus 2.0 array for analysis of over 47,000 transcripts. Sample preparation for array hybridization was carried out as described in the manufacturerâ??s instructions.

2009-05-27 | E-GEOD-16118 | biostudies-arrayexpress

102-Plex Approach for Accurate and Multiplexed Proteome Quantification

Project description:Numerous hyperplexing approaches have been developed to meet the demand for large-scale basic and clinical analysis. Currently, the analysis capacity has expanded to up to 54 samples within a single experiment by utilizing different isotopic and isobaric reagent combinations. In this report, we propose a super multiplexed approach to enable the analysis of up-to 102-plex samples within a single experiment. by the combination of our recently developed TAG-TMTpro and TAG-IBT16 labeling. We systematically investigated the identification and quantification performance of the 102-plex approach using the mixtures of E. coli and HeLa peptides. Our results revealed that all analyses demonstrated accurate and reliable quanti-fication performance. The combination of TAG-TMTpro and TAG-IBT16 approaches expands the multiplexing capacity to 102-plex, providing a more multiplexed quantification method for even larger-scale proteomic analysis.

2024-01-15 | PXD042398 | Pride

Staphylococcus epidermidis strain:102 | isolate:102

Project description:Staphylococcus epidermidis strain:102 | isolate:102 Genome sequencing

| PRJNA1170200 | ENA

Transcriptional profiling of IRF4 -/- vs IRF4 +/- T-cells under Th17 polarizing conditions

Project description:Transcriptional profiling of T-cells isolated from spleen of IRF4 -/- mice and cultured under Th17 polarizing conditions for 42 hrs compared to cells similarly isolated and cultured from spleen of IRF4 +/- mice. The aim of the study was to identify global misexpression of genes in IRF4 -/- cells and hence identify key pathways regulated by IRF4 during Th17 differentiation. Two-condition experiment, IRF4 -/- vs IRF4 +/- Th17 cells at 42hrs. Biological replicates: 3 for each condition

2012-09-13 | E-GEOD-40726 | biostudies-arrayexpress

Flavobacterium sp. 102

Project description:Flavobacterium sp. 102 transcriptome - Chisto_RNA_36

| PRJNA566727 | ENA