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E-GEOD-30543

ABSTRACT: Differential gene expression profiles between SUM149 cells transfected with control siRNA and SUM149 cells transfected with siRNA targeting tarzarotene-induced gene 1 (TIG1)

OTHER RELATED OMICS DATASETS IN: PRJNA144493

PROVIDER: E-GEOD-30543 | ExpressionAtlas | 2025-01-24

REPOSITORIES: ExpressionAtlas

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			Action	DRS
	E-GEOD-30543-analysis-methods.tsv	Tabular
	E-GEOD-30543-atlasExperimentSummary.Rdata	Rdata
	E-GEOD-30543-configuration.xml	Xml
	E-GEOD-30543-percentile-ranks.tsv	Tabular
	E-GEOD-30543.condensed-sdrf.tsv	Tabular

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Homo sapiens

Project description:Differential gene expression profiles between SUM149 cells transfected with control siRNA and SUM149 cells transfected with siRNA targeting tarzarotene-induced gene 1 (TIG1)

| PRJNA144493 | ENA

Differential gene expression profiles between SUM149 cells transfected with control siRNA and SUM149 cells transfected with siRNA targeting tarzarotene-induced gene 1 (TIG1)

2013-12-03 | GSE30543 | GEO

Differential gene expression profiles between SUM149 cells transfected with control siRNA and SUM149 cells transfected with siRNA targeting tarzarotene-induced gene 1 (TIG1)

Project description:We identified tazarotene-induced gene 1 (TIG1) as a potential tumorigenic gene in IBC. To investigate the underlying mechanism by which TIG1 promotes tumor growth and invasiveness of IBC cells, we first sought to identify TIG1 functional partners by using DNA microarray analysis to compare gene expression profiles between SUM149 cells transfected with control siRNA and SUM149 cells transfected with siRNA targeting TIG1. We identified receptor tyrosine kinase Axl as a functional partner of TIG1. SUM149 cells transiently transfected with control siRNA or siRNA targeting TIG1 were used. Total RNA was extracted and purified using RNeasy mini kit (Qiagen, Inc.) according to the manufacturer’s instructions. The integrity of the obtained RNA was assessed using an Agilent 2100 BioAnalyzer (Agilent Technologies). The Affymetrix HGU133 plus platform was used for hybridization, staining, and imaging of the arrays by following the manufacturer’s instructions. Gene expression analysis was performed in triplicate.

2013-12-03 | E-GEOD-30543 | biostudies-arrayexpress

PPARg dependent expression changes during differentiation of 3T3L1 cell into adipocytes

Project description:We profiled PPARg dependent gene expression changes during differntiation of 3T3L1 cell using PPARg siRNA 3T3-L1 (Pre-adipocyte) cell line was induced to differentiate using standard adipocyte differentiation media (IBMX, Dex and Insulin) 48hrs post-confluency. RNA was harvested at day -2 (confluent fibroblasts), 48hrs post-induction with IBMX, DEX and Insulin (day=0) and for each subsequent day after rosiglitazone treatment. Illumina beadchip microarrays were used to determine expression profiles of genes differentially regulated in cells transfected with either siRNA targeting PPARgamma or a non-targeting control siRNA.

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Two human HCC cells (MHCC97H and MHCC97L): PML-siRNA transfected vs. control

Project description:We found PML was responsible for ATO resistance in HCC cells, PML knockdown cells show better sensitivity to ATO treatment. To further explore the mechanism of PML-induced ATO resistance, we performed a microarray assay to compare the differential gene expression profiles of PML-siRNA-treated (PML knockdown) and negative control siRNA-treated cells. Two-condition experiment, PML-siRNA vs. control cells. Biological replicates: two cell lines and each cell line has 1 control, 1 transfected, independently grown and harvested. One replicate per array. Comparisons were made between PML siRNA group and control group for each cell line

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The differentiation/retrodifferentiation program of human U937 leukemia cells is accompanied by changes of VCP/p97

Project description:A possible functional role of VCP/p97 during differentiation of U937 cells was addressed by siRNA-targeting of VCP/p97. Functional changes in VCP-siRNA-transfected cells following phorbol ester-induced monocytic differentiation have been examind by DNA microarray analysis. Cells transfected with the non-targeting AllStars negative siRNA (Qiagen) served as a reference. Keywords: cellular modification design

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High-throughput RNA sequencing analysis of human nasopharyngeal carcinoma cell line HK1 transfected with E2F1 siRNA or E2F3 siRNA

Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are using RNA sequencing analysis to evaluate the effects of si-E2F1 (or E2F3) on the mRNA of human nasopharyngeal carcinoma cell line HK1. Methods: Human nasopharyngeal carcinoma cell line HK1 was transfected with a control non-targeting siRNA to cells or transfected with siRNA targeting E2F1 (or E2F3) for 48 hours in DMEM medium (with 10% serum). Total RNA were extracted and detected by Illumina high-throughput RNA sequencing data analysis. 3 independent biological replicates were plated, transfected in parallel for each control and siRNA. Results: Log-fold changes of up- or down-regulated mRNAs between the control and experiment group were selected with a significance threshold of p<0.05. Conclusions: Our study describes the mRNA changes of human nasopharyngeal carcinoma cell line HK1 transfected with E2F1 (or E2F3) siRNA.

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High-throughput RNA sequencing analysis of human colon cancer cell line HCT116 transfected with LINC00152 siRNA.

Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are using RNA sequencing analysis to evaluate the effects of si-LINC00152 on the mRNA of human colon cancer cell line HCT116. Methods: Human colon cancer cell line HCT116 was transfected with a control non-targeting siRNA to cells or transfected with siRNA targeting LINC00152 for 36 hours in DMEM medium (with 10% serum). Total RNA were extracted and detected by Illumina high-throughput RNA sequencing data analysis. 2 independent biological replicates were plated, transfected in parallel for each control and siRNA. Results: Log-fold changes of up- or down-regulated mRNAs between the control and experiment group were selected with a significance threshold of p<0.05. There are 90 mRNAs were up-regulated and 159 were down-regulated in “si-LINC00152” group comparing to “control” group. Conclusions: Our study describes the mRNA changes of human colon cancer cell line HCT116 transfected with LINC00152 siRNA.

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High-throughput sequencing of 3T3-L1 cells with Kdm5c knockdown

Project description:One day prior to confluency, non-targeting (scramble control) siRNA or Kdm5c siRNA were transfected into 3T3-L1 cells and gene expression was assessed by RNA-seq at 24hr, 48hr, and 72hr post transfection.

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Project description:Transcriptional profiling comparing MiaPaCa2 pancreatic cancer cells transfected with S100PBP siRNA to MiaPaCa2 cells transfected with non-targeting control siRNA

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