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E-MTAB-9848

ABSTRACT: RNAseq of HCT116 p53KO cells transfected with siRNA silencing ZNF84 or negative control with either doxorubicin treatment or untreated, cultured 72h post-transfection

PROVIDER: E-MTAB-9848 | ExpressionAtlas | 2025-01-23

REPOSITORIES: ExpressionAtlas

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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: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

| PRJEB41676 | ENA

HCT116 (CRC): control siRNA vs. ZNF746 siRNA Transfected

Project description:Transcriptional profiling of HCT116 cells compared to untreated control with HCT116 cells transfected with ZNF746 siRNA plasmid. Goal was to determine the effects of ZNF746 gene transfection on CRC progression. Two-condition experiment, HCT116 vs. ZNF746 siRNA.

2019-12-01 | GSE90832 | GEO

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

Identifying the downstream effectors of E2F7 in squamous cell carcinoma (SCC) cells

Project description:Advanced head and neck squamous cell carcinomas (HNSCC) are frequently drug resistant and have a mortality rate of 40%. We have previously shown that E2F7 may contribute to drug sensitivity. In the present study, we conducted an M-bM-^@M-^Somics screen to identify factors that were responsible for E2F7-dependent resistance to anthracyclines by HNSCC. We provide, in vitro, in vivo and patient data that identifies the existence of a novel E2F7/Sphingosine kinase 1/Sphingosine-1-phosphate/AKT axis that regulates sensitivity to anthracyclines in HNSCC. Specifically, we show that E2F7-dependent sensitivity to doxorubicin occurs via induction of the sphingosine kinase 1/AKT axis. We also show that pharmacological inhibition of Sphingosine kinase 1 or AKT sensitizes SCC cells to the cytotoxic actions of doxorubicin in vitro and in vivo. Combined, these findings highlight a novel mechanism through which SCC cells acquire resistance to anthracyclines and identify specific pharmacological combinations that could be used to treat SCC. Duplicate total RNA isolated from i) untreated, KJD cells, ii) 1M-BM-5M doxorubicin-treated KJD cells, iii) control plasmid (pcDNA3) transfected, untreated KJD cells, iv) control plasmid (pcDNA3) transfected, 1M-BM-5M doxorubicin-treated KJD cells, v) E2F7 expression plasmid transfected, untreated KJD cells, vi) E2F7 expression plasmid transfected, 1M-BM-5M doxorubicin-treated KJD cells, vii) untreated, SCC25 cells, viii) 1M-BM-5M doxorubicin-treated SCC25 cells, ix) control siRNA (GFPsiRNA) transfected, untreated SCC25 cells, x) control siRNA (GFPsiRNA) transfected, 1M-BM-5M doxorubicin-treated SCC25 cells, xi) E2F7siRNA transfected, untreated SCC25 cells, xii) E2F7siRNA transfected, 1M-BM-5M doxorubicin-treated SCC25 cells were hybridised to an RNA microarray to identify genes which are downstream of E2F7 and regulate chemosensitivity in SCC.

2014-05-30 | E-GEOD-58074 | biostudies-arrayexpress

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. Expression data from 3 independent HCT116 cutures transfected with either DDX5si2008, DDX5si2053, or EBNA1si1666 and 2 independent cultures transfected with mock conditions (no siRNA) were obtained from RNA samples prepared 24hrs post-siRNA transfection. These cultures were seeded with 200,000 cells per well 24hrs prior to siRNA transfection and were grown in DMEM media supplemented with 10% fetal bovone serum. Transfections were performed using lipofectamine RNAiMAX (Invitrogen 13778-075) and the manufacturer's protocol.

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

Gene expression data from the HCT-116 colon cancer cell line in the presence or absence of siRNA targeting APC

Project description:Gene expression data were collected by RNA-seq from HCT-116 cells in the presence or absence of siRNA targeting APC and 1,376 transcripts changed in expression following APC silencing were identified relative to scrambled siRNA-transfected and untreated controls.

2018-05-24 | GSE99263 | GEO

Homo sapiens

Project description:HCT116 (CRC): control siRNA vs. ZNF746 siRNA Transfected

| PRJNA356271 | ENA

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

2012-06-02 | GSE36141 | GEO

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

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