Pyknon siRNA transfection compared with empty vector
ABSTRACT: We designed siRNAs against pyk-reg-90 and pyk-reg-10 using the Dharmacon algorithm (Dharmacon siDESIGN http://www.dharmacon.com/sidesign/). Each of four highest-ranking siRNA sequences for pyk-reg-90 and pyk-reg-10 respectively was tested in our and pyk-reg-90, we used a pool of different siRNAs that included the two most effective siRNAs. The cellsperformance was assessed at 24-hr intervals until 96 hrs posttransfection by qRT-PCR. For both pyk-reg-10resuspended in 1X siRNA buffer (Dharmacon, LaFayette CO, USA) to a stock concentration of 50 ?M. Theexperiments. These siRNAs were were transfected with the corresponding siRNA pool at the final concentration of 100nM and 200nM by using Lipofectamine 2000 (Invitrogen) according to the manufacturer's protocol for further analysis. As control, we used a pool of non-targetting siRNAs (Dharmacon).
Project description:IL-33 is a nuclear cytokine from the IL-1 family that plays important roles in health and disease. Under healthy conditions, IL-33 is constitutively expressed to high levels in the nucleus of producing cells in various human and mouse tissues. The extracellular function of IL-33 cytokine has been well documented, but it remains unclear whether intracellular nuclear IL-33 has additional functions in the nucleus. Here, we used a global proteomic approach based on quantification of 5000 individual proteins by high-resolution mass spectrometry to compare the extracellular and intracellular roles of IL-33 in primary human endothelial cells, a major source of IL-33 protein in human tissues. Large-scale analysis of protein expression was performed either after stimulation of the cells with the IL-33 mature form IL-3395-270 (during 6h or 24h) or after siRNA knockdown of intracellular IL-33 (two experiments, each with a different pool of distinct siRNAs, noted siRNA1 and siRNA2). In each case, proteins were fractionated by 1D SDS-PAGE in 12 gel bands, and label-free quantitative analysis was performed. The present dataset contains the files for the two experiments of knockdown of endogenous nuclear IL-33 expression: - RNA silencing strategy 1. Knockdown of endogenous nuclear IL-33 expression was performed with a pool of four distinct siRNAs (Dharmacon ON-TARGETplus SMARTpool IL-33 siRNAs) that have been specifically modified for efficient silencing of the target gene with reduced off-target effects. Cells transfected with these siRNA duplexes (si1) were compared with those transfected with the provided controls (CTsi1). Three independent biological replicates (noted _A, _B, _C) were prepared and analyzed for each condition, leading to 6 different samples. Each of them was fractionated into 12 gel bands analyzed by nanoLC-MS/MS, leading to 72 raw files. - RNA silencing strategy 2. The second knockdown strategy was based on the use of an independent pool of three siRNAs targeting IL-33, predesigned by another provider using new and critical siRNA design rules (Sigma MISSION Predesigned Il-33 siRNAs based on Rosetta siRNA design algorithm). Cells transfected with these siRNA duplexes (si2) were compared with those transfected with the provided controls (CTsi2). Three independent biological replicates (noted _A, _B, _C) were prepared and analyzed for each condition, leading to 6 different samples. Each of them was fractionated into 12 gel bands analyzed by nanoLC-MS/MS, leading to 72 raw files.
Project description:HNF4a is an important liver transcription factor that regulates at least a thousand genes in the liver. Here we used expression profiling in HepG2 cells, a hepatocellular carcinoma cell line, in which HNF4a was knocked down by RNAi to identify some of those target genes. This dataset accompanies the article in Hepatology 2010 Feb;51(2):642-53. Integrated approach for the identification of human hepatocyte nuclear factor 4alpha target genes using protein binding microarrays by Bolotin E, Liao H, Ta TC, Yang C, Hwang-Verslues W, Evans JR, Jiang T, Sladek FM. RNA interference (RNAi) against HNF4a2 was performed in HepG2 cells using small, interfering RNAs (siRNAs) corresponding to nucleotides +179 to +197 of human HNF4A (NM_178849, sense siRNA: 5'-UGUGCAGGUGUUGACGAUGdTdT-3', antisense siRNA 5'-CAUCGUCAACACCUGCACAdTdT-3') (Dharmacon, Lafayette, CO). Total RNA was extracted with Trizol (Life Technologies, Carlsbad, CA) and reverse transcribed with the Reverse Transcription System (Promega, Madison, WI). Polymerase chain reaction (PCR) amplification was performed in the linear range (see Supporting Table 3B for a list of PCR primers). Expression profiling analysis was performed with Affymetrix oligonucleotide arrays (HGU133 Plus 2.0) using RNA from control (PGL3 siRNA) or treated (HNF4a siRNA) HepG2 cells
Project description:Signal transducer and activator of transcription 3 (STAT3) is altered in several epithelial cancers and represents a potential therapeutic target. Here, STAT3 expression, activity and cellular functions were examined in two main histotypes of esophageal carcinomas. In situ, immunohistochemistry for STAT3 and STAT3-Tyr705 phosphorylation (P-STAT3) in esophageal squamous cell carcinomas (ESCC) and Barrett’s adenocarcinomas (BAC) revealed similar STAT3 expression in ESCCs and BACs, but preferentially activated P-STAT3 in ESCCs. In vitro, strong STAT3 activation was seen by EGF-stimulation in OE21 (ESCC) cells, whilst OE33 (BAC) cells showed constitutive weak STAT3 activation. STAT3 knockdown significantly reduced cell proliferation of OE21 and OE33 cells and reduced cell migration in OE33, but not in OE21 cells. Transcriptome analysis identified STAT3-knockdown associated down-regulation of cell cycle processes and the selective down-regulation of cyclins and cyclin dependent kinaes associated genes in both OE21 and OE33 cells. Moreover, the transcriptome response showed changes in cell migration/invasion related genes that correlated with the associated phenotype measurements. This study demonstrates the importance of STAT3 expression and activation in esophageal carcinomas, whereby the extent differs between ESCCs and BACs. STAT3 knockdown significantly reduces cell proliferation in both types of esophageal cancer cells and inhibits migration in BAC cells. Thus, STAT3 may be further exploited as potential novel therapeutic target for esophageal cancers. The effect of STAT3 knock-down in OE33 and OE21 cells was calculated from three biologically independent experiments. 3x10e4 cells were seeded in triplicate in 24 well-plates and were transfected with twice 100nM STAT3 siRNA (pool of 4 STAT3 sequences, siGENOME®SMARTpool®, Dharmacon RNAi Technologies, Thermo Fisher Scientific, Lafayette, USA) or Silencer® negative siRNA control (Invitrogen/Life Technologies GmbH, Darmstadt, Germany) using 1µl DharmaFECT (Dharmacon RNAi Technologies, Thermo Fisher Scientific, Lafayette, USA) transfection reagent for OE33 cells or siPORTTM NeoFXTM (Invitrogen/Life Technologies GmbH, Darmstadt, Germany) transfection reagent for OE21 cells. Differential gene regulation was quantified 72 hours after the first transfection by comparing separately for the OE21 and OE33 cells the STAT3 siRNA replicates and the respective cell lines containing the scrambled siRNA vector.
Project description:The involvement of thousands of genes complicates the identification of clinically relevant candidate genes in common diseases. We hypothesized that genes co-regulated with a key gene in allergy, IL13, would form a module that could help to discover novel candidate genes. We identified a Th2 cell module by siRNA mediated knock down of 25 putative IL13-regulating transcription factors (TFs) followed by expression profiling. Human CD4+ T cells (hBP CD4+ T cells, 2W-200, Lonza, Vallensbak Strand, Denkmark) were nucleofected either with nucleofection buffer, 1 µM human on target plus SMART pool siRNA against ELK1, GATA3, NFATC3, MAF, NFKB1, JUN, STAT3 (Dharmacon, Lafayette, CO) or non-targeting siRNA using the AMAXA nucleofection program U-014. Six hours after then nucleofection cells were washed, activated and polarized towards Th2. The CD4+ cells were activated with plate bound anti-CD3 (500ng / ml for coating of the plate), with soluble anti-CD28 (500ng / ml) and with IL-2 (17ng /ml, all purchased from R&D). Th2 polarization was induced with anti-IL-12 (5µg/ml) and IL-4 (10ng / ml). For RT-PCR and microarray analyisis the cells were harvested 12 hours of polarization and total RNA was extracted.
Project description:HeLa cells were cultured in 6-well tissue culture plates (~2x105 cells/well) in DMEM medium containing 10% fetal bovine serum. Arp8 siRNA (sc-60072) was obtained from Santa Cruz, while all specific siRNAs including non-targeting siRNA (D-001206), Ino80 siRNA (D-004176), Ies6 siRNA (D-019327) and Ies2 siRNA (D-009848) SMART pool were from Dharmacon (U.S.A.). The cells were transiently transfected with 10~20 pmol specific siRNAs using Lipofetamine RNAMAX transfection kit (Invitrogen, Cat.No-864425) following the manufacture’s instruction. 24 hours after transfection, cells were divided into new 6-well plates for western blot, RT-PCR, and DNA microarray analysis. 48 hours after siRNAs transfection, cells were harvested and lysed. Whole-cell extract (WCE) were prepared by adding 4 x SDS sample buffer, and total RNA was isolated using TRIzol® LS Reagent (Invitrogen). In addition, cells from 1 well of a 6-well plate were rinsed twice with warm PBS and harvested. Cells were then stored in an RNA hold solution (ER501-01, Beijing Transgen Biotech Co., Ltd.). After the knockdown efficiency was confirmed, cells in RNA hold solution were sent to EMTD Science and Technology Development Co., Ltd. (Beijing, China) for DNA microarray analysis. Overall design: RNA obtained from knock down four subunits of human INO80 complex in Hela cells and control sample
Project description:SH-SY5Y cells were transfected with an siRNA against T-UC.300A (final concentration 50nM) or negative control siRNA (Dharmacon Negative Control #1, final concentration 50 nM) using the transfection reagent Lipofectamine (Invitrogen). Media was changed after 24hrs. RNA was extracted 120hrs after transfection. Gene expression microarray analysis was carried out using Roche NimbleGens 4x72K Homo Sapiens gene expression array.
Project description:SH-EP cells were depleted for ZBTB4; Transfection of the cells were performed by oligofectamin RNAimax (Invitrogen) with siRNA smart pool (Dharmacon RNA Technologies); total RNA was isolated using RNAeasy Mini Kit (QIAGEN), preamplified, labeled with Cy3 and Cy5, respectively, and hybridized to cDNA-microarrays
Project description:In addition to mediating sister chromatid cohesion, cohesin plays a central role in DNA looping and segmentation of the genome into contact domains (TADs). Two variant cohesin complexes that contain either STAG/SA1 or SA2 are present in all cell types. Here we addressed their specific contribution to genome architecture in non-transformed human cells. We found that cohesin-SA1 drives stacking of cohesin rings at CTCF-bound sites and thereby contributes to the stabilization and preservation of TAD boundaries. In contrast, a more dynamic cohesin-SA2 promotes cell type-specific contacts between enhancers and promoters within TADs independently of CTCF. SA2 loss, a condition frequently observed in cancer cells, results in increased intra-TAD interactions, likely altering the expression of key cell identity genes. Overall design: ChIP-seq for cohesin subunits SMC1, SA1 and SA2 was performed in 3 different cell lines (MCF10A, HMEC, HCAEC) and peak calling was done against the input sample from the corresponding cell line. RNA-seq was performed in triplicates in MCF10A cells control depleated from SA1, SA2 or CTCF by means of Dharmacon SMART pool siRNAs. HiC-seq was performed in two replicates in MCF10A cells control and depleated from SA1 and SA2 by means of Dharmacon SMART pool siRNAs. 4C-seq was performed in MCF10A cells control and depleated from SA2 or CTCF.
Project description:Ma-Mel-15 human melanoma cell cultures were transiently transfected (RNAiMax, Lipofectamin) with control siRNA, siRNA against MITF (pool of 4 siRNAs), siRNA against c-JUN (pool of 4 siRNAs) or combinations of siMITF and siJUN. Cells were then either treated with TNF-alpha (1000U/ml) for 24 hours or left untreated. The experiment was performed as biological duplicates. We aimed to determine how c-JUN cooperates with acute MITF-loss in human melanoma cells to increase inflammatory responsiveness and cell plasticity. Total RNA was obtained from siRNA/TNF-treated Ma-Mel-15 melanoma cell lines and global gene expression profiling was done using the Illumina Human HT12 v4 platform.
Project description:Mouse models of cancer recapitulate many of the molecular and biological features of the human disease. We sought to exploit these experimental merits in a systematic comparative proteomics search for circulating proteins associated with lung tumor development. In-depth quantitative proteomics was applied to plasmas from three mouse models of lung adenocarcinoma driven by mutant EGFR or Kras or induced by urethane exposure and a mouse model of small cell lung cancer driven by loss of Trp53 and Rb. To further refine our lung cancer-specific and broad carcinoma signatures, we intersected these lung cancer proteome profiles with those from other well-established mouse models of pancreatic, ovarian, colon, prostate and breast cancer, as well as two mouse models of inflammation. A set of proteins regulated by Titf1/Nkx2-1, a master transcription factor in cells from the peripheral airways and a known lineage-survival oncogene in lung cancer was identified in plasmas of mouse models of lung adenocarcinoma. An EGFR network of proteins was discerned in the plasma of mice with lung tumors driven by a mutant human EGFR. Levels of these proteins returned toward baseline upon treatment with a tyrosine kinase inhibitor. Moreover, a distinct plasma signature was uncovered in the Trp53/Rb mutant small cell lung cancer model that included a set of proteins associated with neuroendocrine development. Our studies have identified novel plasma protein signatures among molecularly or histopathologically defined lung cancer subtypes. Overall design: siRNA transfection experiments were performed in NCI-H3255 and HCC4019 lung adenocarcinoma cell lines using ON-TARGETplus SMARTpool small interfering RNAs (siRNAs) targeting TITF1 (L-019105-01-0005) along with a negative control (ON-TARGETplus siCONTROL nontargeting siRNA pool; D-001810-10-05) obtained from Dharmacon. 400000 cells were seeded in antibiotic-free RPMI-1640 media supplemented with 10% FBS, in 6-well culture plates. The next day, cells were transfected at a final concentration of 100nM siRNA using 6ul DharmaFECT 1 (Dharmacon) according to the manufacturer's instructions. 72-hours post-transfection, RNA was harvested using Trizol (Invitrogen) and protein using RIPA buffer for microarray expression and western blotting, respectively. RNA from TITF1 knockdown and control experiments was profiled by the MSKCC Genomics Core using the Illumina Human HT-12 v3.0 array platform according to manufacturer's instructions. Two biological replicates were profiled for each condition. Resulting data files were exported using GenomeStudio software, log2 transformed, quantile-normalized and analyzed using Partek Genomics Suite (v6.5). Average values of replicates for each gene were then compared between the TITF1 knockdown and non-targeting treatments for each cell line to identify candidate TITF1 regulated genes.