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Unknown,Transcriptomics,Genomics,Proteomics

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Effects of supernatants of USP2 knockdown HL-60 cells and mock transfected HL60 cells on differentiated 3T3-L1 cells

ABSTRACT: Ubiquitin specifc protease (USP) 2 modulates various cellular responces including carcinogenesis, spermatogenesis, and glucose metabolism. So far, we established USP2 knockdown HL-60 cells to explore roles of USP2 in macrophages. In this experiment, we investigated whether USP2 knockdown HL-60 cells more prominently modulate function of adipocytes compared with control cells. USP2 knock down(KD) HL-60 cells and mock vector-transfected mock control cells were differentiated into macrophage-like cells in the presence of 30nM of phorbol 12-myristate 13-acetate for 5 days. Subseqently, supernatants of the USP2 KD cells and control cells were added to differentiated 3T3-L1 cells for 3 and 6 hrs. Total RNA was isolated from the supernatant-treated 3T3-L1 cells, and subjected to microarray analysis. Duplicate samples were prepared for each cell and time point.

ORGANISM(S): Mus musculus

SUBMITTER: Hiroshi Kitamura

PROVIDER: E-GEOD-43313 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Effects of supernatants of USP2 knockdown HL-60 cells and mock transfected HL60 cells on differentiated 3T3-L1 cells

Project description:Ubiquitin specifc protease (USP) 2 modulates various cellular responces including carcinogenesis, spermatogenesis, and glucose metabolism. So far, we established USP2 knockdown HL-60 cells to explore roles of USP2 in macrophages. In this experiment, we investigated whether USP2 knockdown HL-60 cells more prominently modulate function of adipocytes compared with control cells.

2013-08-27 | GSE43313 | GEO

Mus musculus

Project description:Effects of supernatants of USP2 knockdown HL-60 cells and mock transfected HL60 cells on differentiated 3T3-L1 cells

| PRJNA185411 | ENA

Transcriptional response to stress in serum deprived mouse fibroblasts

Project description:We have employed gene expression profiling in order to identify targets of transcriptional response to stress in mouse Swiss 3T3 fibroblasts, where we induced p38/MAP kinase pathway using anisomycin. Serum starved (72 h) mouse 3T3 cells were treated with anisomycin (188.5 nM) for 1, 3, and 6 h (in triplicates). Untreated, serum-starved cells were used as a control. RNA was collected and gene expression profiling using mouse Agilent expression array (4x44k) was performed.

2014-08-12 | E-GEOD-55554 | biostudies-arrayexpress

Whole transcriptomic analysis of mouse embryonic fibroblasts BALB/c 3T3 clone A31-1-1 after treatment with bis (2-ethylhexyl) phthalate for 24 hrs

Project description:Di(2-ethylhexyl) phthalate (DEHP; CAS No. 117-81-7) belongs to the phthalate class of chemicals, and is commonly added to plastics for flexibility. DEHP has been identified as an index compound for group-TDI calculations owing to its extensive toxicological dataset. Humans are exposed to this ubiquitous environmental contaminant through multiple routes. DEHP has been designated as probably and possibly carcinogenic to humans based on its ability to induce rodent carcinogenicity, although the relevance of its mode of action (MoA) in humans remains unclear. The aim of this study was to investigate the carcinogenic potential of DEHP using an alternative method and explore the possible mode and mechanisms of action at the molecular level. Special attention has been paid to DEHP dissolution in cell media, leading to the use of a final concentration of 0.5% DMSO. Transcriptomics were conducted on cells treated with a cytotoxic concentration of DEHP (19.7 µg/mL) for 24 h. The aim of the microarray experiment was to analyze the molecular effects of the substance under the specific conditions of the Cell Transformation Assay protocol (BALB c/ 3T3 clone A31-1-1 CTA, according to the method validated by ECVAM, Sasaki et al., 2012), in order to provide mechanistic explanations of the test results derived from the CTA.

2024-06-17 | E-MTAB-13716 | biostudies-arrayexpress

Transcription profiling of mouse NIH-3T3 cells treated with interferon alpha or gamma

Project description:Expression data from NIH-3T3 cells treated with mock, 100 U/ml IFN alpha or 100 U/ml gamma for 1 or 3h on nt-RNA labeled for 30-60 min at different times of interferon treatment; Differential gene expression caused by IFN alpha or gamma was analyzed in newly transcribed RNA (nt-RNA) of NIH-3T3 cells treated for 1 or 3 h. RNA was labeled for 30 to 60 min and separated from total cellular RNA (tc-RNA) following Trizol RNA preparation and thiol-specific biotinylation; We used microarrays to analyze the effects of IFNalpha and gamma treatment in newly transcribed RNA (nt-RNA) Experiment Overall Design: NIH-3T3 cells (5th to 15th passage after thawing) were split 24 h before start of the experiment. When starting the experiment 80% confluency was reached. The experiment was started by applying fresh, prewarmed, CO2-equilibrated medium containing either mock, 100U/ml IFN alpha or 100 U/ml IFN gamma. Labeling was either started simultaneously, 30 or 150 minutes later.

2009-10-11 | E-GEOD-9975 | biostudies-arrayexpress

Transcriptional analysis of live and hybridized J1 and NIH-3T3 cells

Project description:J1 mouse embryonic stem cells (mESCs) and NIH-3T3 fibroblasts were grown in standard media conditions. Hybridized cells were fixed with 4% paraformaldehyde; incubated for 12 hours at 30C in an RNA preserving hybridization (RPH) buffer (300 mM Sodium chloride, 30mM Sodium citrate, 2.1M Ammonium sulfate, 25% formamide, 10 mM EDTA, 1 mg/ml E. Coli tRNA, 500 μg/ml BSA); and reverse cross-linked for 1 hour at 50C in with Sodium dodecyl sulfate (SDS) and Proteinase K (100 mM NaCl, 10 mM pH 8.0 Tris, 1 mM EDTA, 0.5% SDS, 500 μg/ml Proteinase K). one replicate per sample

2014-03-20 | E-GEOD-55919 | biostudies-arrayexpress

Human HL-60 Cells: all-trans retinoic acid (ATRA) vs. ATRA plus arsenic trioxide (ATO)

Project description:Transcriptional profiling of human leukemia　HL-60 cells comparing ATRA treated HL-60 cells with ATRA plus ATO. Goal was to determine the effects of ATO on ATRA induced differentiation of HL-60 cells.

2015-03-31 | GSE67420 | GEO

Human HL-60 Cells: all-trans retinoic acid (ATRA) vs. ATRA plus arsenic trioxide (ATO)

Project description:Transcriptional profiling of human leukemia?HL-60 cells comparing ATRA treated HL-60 cells with ATRA plus ATO. Goal was to determine the effects of ATO on ATRA induced differentiation of HL-60 cells. Two-condition experiment, ATRA vs. ATRA plus ATO treated HL-60 cells.

2015-03-31 | E-GEOD-67420 | biostudies-arrayexpress

Identification of genes differentially expressed in HAX1-deficient HL-60 cells

Project description:RNA sequencing was performed to compare levels of intracellular transcripts in HL-60 WT and HL-60 HAX1 KO cells. Experiment was performed to check influence of HAX1 protein on cellular transcriptome (in HL-60 cell line)

2022-09-21 | GSE189609 | GEO

LSD1 knockdown in 3T3-L1 preadipocytes

Project description:Obesity is often associated with a low-grade systemic inflammation state that contributes to the development of insulin resistance and atherosclerotic complications. This is usually coupled with increased macrophage infiltration in the adipose tissue and a defect in adipocyte differentiation that results in accumulation of hypertrophic fat cells characterized by a deregulated pattern of adipokine expression. Here we show that knockdown of histone demethylase lsd1 in 3T3-L1 preadipocytes results in defective adipogenesis and derepression of an inflammatory program in these cells. The dataset consists of four sample groups: [1] 3T3-L1 preadipocytes (passage 19) transfected with a control scrambled siRNA at 24h after transfection (siC.24h), [2] 3T3-L1 preadipocytes (p.19) transfected with a siRNA directed against LSD1 at 24h after transfection (siLsd1.24h), [3] 3T3-L1 preadipocytes (p.21) transfected with a control scrambled siRNA at 48h after transfection (siC.48h), and [4] 3T3-L1 preadipocytes (p.21) transfected with a siRNA directed against LSD1 at 48h after transfection (siLsd1.48h). The 24h sample groups (siC.24h and siLsd1.24h) consist of two biological replicate samples; the 48h sample groups (siC.48h and siLsd1.48h) consist of three biological replicate samples. Each sample was hybridized to a separate array, for a total of ten arrays.

2013-12-31 | E-GEOD-25423 | biostudies-arrayexpress

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