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RNAseq of HCT116 p53KO cells transfected with either siRNA silencing ZNF84 or with negative control siRNA, in 2 variants of experiment a) with doxorubicin treatment (doxorubicin added 48h post-transfection, for the next 48h before harvesting) b) untreated, cultured 72h post-transfection

ABSTRACT: RNAseq of HCT116 p53KO cells transfected with either siRNA silencing ZNF84 or with negative control siRNA, in 2 variants of experiment a) with doxorubicin treatment (doxorubicin added 48h post-transfection, for the next 48h before harvesting) b) untreated, cultured 72h post-transfection

PROVIDER: PRJEB41676 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR4904500.fastq.gz	Fastqsanger.gz
	ERR4904501.fastq.gz	Fastqsanger.gz
	ERR4904492.fastq.gz	Fastqsanger.gz
	ERR4904502.fastq.gz	Fastqsanger.gz
	ERR4904493.fastq.gz	Fastqsanger.gz

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RNAseq of HCT116 p53KO cells transfected with either siRNA silencing ZNF84 or with negative control siRNA, in 2 variants of experiment a) with doxorubicin treatment (doxorubicin added 48h post-transfection, for the next 48h before harvesting) b) untreated, cultured 72h post-transfection

Project description:The aim of this experiments was to characterise the transcriptomic changes occurring in cancer cells, in which ZNF84 gene is silenced, in control conditions and when cells undergo stress by being treated with cytostatic doses of doxorubicin. We anticipated that ZNF84 regulates the level of p21 cell cycle inhibitor and therefore contributes to senescence induction in response to stress. We wanted to know whether attenuation of senescence in cells with downregulated ZNF84 is accompanied by alterations in other biological processes and signalling pathways. Cells were transfected with 30 nM siRNA (against ZNF84 or negative control siRNA) and then either a) doxorubicin was added (48 hours after transfection and cells were cultured in the presence of the drug for another 48 hours) b) no drug was added (cells were cultured in drug-free medium for 72 hours post- transfection) Variants a) and b) were separate RNA sequencing experiments.

2021-05-05 | E-MTAB-9848 | biostudies-arrayexpress

RNA-seq for siRNA 48h

Project description:RNA-seq for siRNA 48h

| PRJNA742365 | ENA

Expression analysis of C2C12 cells treated with scramble siRNA or siRNA directed against Brd4

Project description:We transfected C2C12 cells with 100nM of scrambled siRNA scramble and an siRNA directed against Brd4. Cells were harvested at 48h post-transfection and RNAseq was performed with polyA selection

2022-09-28 | GSE141777 | GEO

Expression analysis of C2C12 cells treated with scramble siRNA or siRNA directed against Fndc1

Project description:We transfected C2C12 cells with 100nM of scrambled siRNA scramble and an siRNA directed against Fndc1. Cells were harvested at 48h post-transfection and RNAseq was performed with polyA selection

2024-08-17 | GSE217125 | GEO

Gene expression data at 24hrs post-siRNA transfection for HCT116 cultures transfected with either DDX5si2008, DDX5si2053, or EBNA1si1666 siRNA's or mock transfected.

Project description:HCT116 cells were transfected with two different siRNA's targeting either DDX5, an siRNA targeting EBNA1, or no siRNA (mock). The siRNA targeting EBNA1 is used as a negative control since HCT116 cells do not have the EBNA1 gene. RNA was obtained from cultures at 24hrs post-siRNA transfection using the Qiagen RNeasy Minikit (cat. # 74104) with on-column DNase digestion performed as per the manufacturer's protocol. The RNA samples were isolated at 24hrs post-siRNA transfection since this timepoint precedes an impaired G1-to-S phase cell cycle progression phenotype that is evident at 48hrs post-siRNA transfection and so may reveal gene expression changes occuring before this effect on cell cycle. RNA samples were submitted to the Cold Spring Harbor Laboratory Microarray Faciity where cDNA was prepared, labeled, and hybridized to Affymetrix GeneChip Human Gene 1.0 ST microarrays. Data from the arrays were processed using the RMA method with an up-to-data probe set definition (Biostatistics 4:249-264 and Nucleic Acids Research 33(20):e175. Gene set analysis was performed using generally applicable gene set enrichment (BMC Bioinformatics 10:161). The most differentially regulated gene ontology groups were selected with FDR q-value < 0.1.

2012-06-02 | GSE36141 | GEO

Gene expression data at 24hrs post-siRNA transfection for HCT116 cultures transfected with either DDX5si2008, DDX5si2053, or EBNA1si1666 siRNA's or mock transfected.

2012-06-01 | E-GEOD-36141 | biostudies-arrayexpress

EWS-FLI1-transfection of HEK293

Project description:Response of HEK293-cells after transfection with EWS-FLI1. HEK293 cells were transfected with the expression vector pIRES2-EGFP containing type I EWS-FLI1 or empty control vector. For transient transfection standard DEAE dextran method was used and RNA was isolated 48h post transfection. For stable transfection cells were transfected using FuGENE 6 (Roche, Mannheim, Germany) and cells were selected with 400 ug/mL G418. DNA-microarray analysis was performed using Affymetrix HG-U133A microarrays.(see Staege et al. Cancer Res. 2004) Keywords = HEK293 Keywords = EWS-FLI1 Keywords = Ewing family tumors Keywords: other

2004-10-07 | GSE1822 | GEO

RNA-seq data for non-targeting siRNA and CDK11 siRNA transfection in SHhES8 cells

Project description:RNA-seq data for non-targeting siRNA and CDK11 siRNA transfection in SHhES8 cells

| PRJNA508721 | ENA

CHD6 transcriptome

Project description:HEK293T cells were transfected with plasmids expressing a control siRNA or a siRNA especific for CHD6 protein. 48H post-transfection, total RNA was isolated and used for transcriptome analysis. Four biological replicates carried out by triplicate were used.

2018-01-31 | GSE109848 | GEO

Differential expression of genes after transfection of STAT6 specific siRNA in NCI-H460 cells

Project description:The experiment was designed to identify the genes which get altered after the transfection of siRNA targeting STAT6 in NCI-H460 cells. The NCI-H460 cells plated in 12-well plate were transfected with 60nM of STAT6 specific siRNA.

2011-12-01 | GSE25942 | GEO

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