Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

13 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

MiRNA microarray analysis of human squamous cell lung cancer cells-H226 transfected with DDX56 siRNA and control siRNA

ABSTRACT: H226 cells transfected with DDX56 siRNA and control siRNA were incubated for 48 hours and miRNA isolated using miRNeasy mini kit (Qiagen) according to the manufacturer’s instructions. miRNA expression profiling was conducted using the Agilent Human miRNA (8×60K) Microarray (Agilent Technologies).

ORGANISM(S): Homo sapiens

SUBMITTER: Qingqing Wu

PROVIDER: E-MTAB-6676 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Microarray analysis of human squamous cell lung cancer-H226 cells transfected with DDX56 siRNA and control siRNA

Project description:H226 cells transfected with DDX56 siRNA and control siRNA were incubated for 48 hours and total RNA isolated and used for the microarray analysis using Affymetrix Human U133 Plus 2.0 Arrays. Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 4.0 (Affymetrix, Santa Clara, CA, US) with default settings.

2019-07-01 | E-MTAB-6675 | biostudies-arrayexpress

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

iTRAQ MS of mouse LbetaT2 cells transfected with Galphas siRNA vs. scrambled siRNA

Project description:Twenty million LbetaT2 cells were transfected with either control or Galphas siRNA, then were seeded in 100-mm cell culture plates in DMEM + 10% FBS. Two days later, cells were washed twice with pre-warmed PBS. Conditioned media was harvested another 24 h later, and centrifuged at 20,000 g for 10 min at 4°C to remove cell debris. To enrich secreted proteins in the conditioned media, conditioned media samples were centrifuged using Amicon centrifugal filters with a 3kDa cutoff (Millipore, Billerica, MA). A total of 8 concentrated conditioned media samples were independently prepared: 4 samples from control siRNA-treated cells, and 4 samples from Galphas siRNA-treated cells. Samples were stored at –70°C until they were sent to the Mount Sinai Proteomics Core Facility.HPLC-isobaric tags for relative and absolute quantitation mass-spectrometry (iTRAQ MS) - Data analysis ProteinPilot 3.0 (AB Sciex) was used to search the MS/MS spectra for protein identification and quantitation with its searching algorithm Paragon 3.0.0.0 (*Reference). The protein database used for searching was Uniprot mouse fasta file (release-2010_11). The search parameters include quantitation for iTRAQ 8-plex (peptide-labeled), MMTS for cysteine alkylation, trypsin for enzyme digestion, biological modifications for ID focus, and taxonomy set for Mus musculus. The detected protein threshold was set to 1.3 (95% confidence). Additionally, we converted our AB Sciex mass spectral data (TOF/TOF data) into an mzML format, using the AB Sciex MS Data Converter (beta version 1.3) tool. Finally, we used the command line tool group2xml, which is included with ProteinPilot Software, to convert the .group search engine result file to an XML file.

2016-09-27 | PXD000063 | Pride

Human pulmonary microvascular endothelial cells (HPMECs): Control siRNA vs HSP27 siRNA

Project description:Transcriptional profiling of HPMECs comparing Control siRNA treated with HSP27 siRNA Two-condition experiment, control siRNA vs HSP27 siRNA ; 3 controlsiRNA transfected replicates , 3HSP27 siRNA replicates. Replicates were pooled and hybridized to a single array.

2015-08-29 | E-GEOD-72485 | biostudies-arrayexpress

miRNA expression profiles of PRC SiRNA vs scramble transfected XTC.UC1 cells

Project description:PGC-1 related coactivator (PRC) shares structural and functional features with PGC-1{alpha}. It regulates several metabolic pathways and mitochondrial biogenesis. Its specific role in the early programming of cell proliferation suggests a finely regulated crosstalk between the mitochondrial functions and the cell cycle status. To explore the PRC-regulated pathways, we used a cell-line model of mitochondrial-rich tumors, presenting an oxidative metabolism and a specific increase in PRC expression. We looked for the feedback loop exerted by miRNAs on the regulation of PRC-related mitochondiral functions Expression profiles of miRNA at 48h PRC SIRNA treatment compared to scramble in XTC.UC1 cells. In duplicate.

2011-11-22 | E-GEOD-33843 | biostudies-arrayexpress

Differential gene expression in neuroblastoma cells after transfection with control siRNA, N-Myc siRNA-1, N-Myc siRNA-2, lncMycN siRNA-1 or lncMycN siRNA-2

Project description:N-Myc oncoprotein induces neuroblastoma by modulating gene transcription, and long noncoding RNAs exert biological effects by regulating gene expression. We analysed whether N-Myc and the long noncoding RNA lncMycN mediate the expression of common subsets of genes. Neuroblastoma Kelly cells were transfected with control siRNA, N-Myc siRNA-1, N-Myc siRNA-2, lncMycN siRNA-1 or lncMycN siRNA-2. RNA was extracted from the cells 48 hours after siRNA transfections, and subjected to differential gene expression studies with Affymetrix microarrays.

2015-03-31 | E-GEOD-50959 | biostudies-arrayexpress

siRNA profiling of HeLa cells reveals strand-specific 5-O-methylation of siRNA duplexes controls guide strand selection and targeting specificity.

Project description:Small interfering RNAs (siRNAs) and microRNAs (miRNAs) guide catalytic sequence-specific cleavage of fully or nearly fully complementary target mRNAs or control translation and/or stability of many mRNAs that share 6-8 nucleotides (nt) of complementarity to the siRNA and miRNA 5' end. siRNA- and miRNA-containing ribonucleoprotein silencing complexes are assembled from double-stranded 21- to 23-nt RNase III processing intermediates that carry 5' phosphates and 2-nt overhangs with free 3' hydroxyl groups. Despite the structural symmetry of a duplex siRNA, the nucleotide sequence asymmetry can generate a bias for preferred loading of one of the two duplex-forming strands into the RNA-induced silencing complex (RISC). Here we show that the 5'-phosphorylation status of the siRNA strands also acts as an important determinant for strand selection. 5'-O-methylated siRNA duplexes refractory to 5' phosphorylation were examined for their biases in siRNA strand selection. Asymmetric, single methylation of siRNA duplexes reduced the occupancy of the silencing complex by the methylated strand with concomitant elimination of its off-targeting signature and enhanced off-targeting signature of the phosphorylated strand. Methylation of both siRNA strands reduced but did not completely abolish RNA silencing, without affecting strand selection relative to that of the unmodified siRNA. We conclude that asymmetric 5' modification of siRNA duplexes can be useful for controlling targeting specificity. Experiment Overall Design: For details please see: Chen PY, Weinmann L, Gaidatzis D, Pei Y, Zavolan M, Tuschl T, Meister G. RNA (2008) 14(2):263-74.

2008-06-11 | E-GEOD-10960 | biostudies-arrayexpress

Expression Profiles of Primary Mouse Hepatocytes treated with Cyclosporin A and solvent control [miRNA]

Project description:The microRNA changes induced in Primary Mouse Hepatocytes of C57Bl6-mice by Cyclosporin A after treatment for 24h and 48h The study investigated differential microRNA expression in Primary Mouse Hepatocytes following 24 and 48 hours of exposure to Cyclosporin A and solvent. Three biological replicates per compound/six per solvent. In total 24 arrays .

2014-07-24 | E-GEOD-55880 | biostudies-arrayexpress

Nanopore RNA-seq of human osteosarcoma cell line U2OS treated with siRNA against MDC1, PLRG1, or control siRNA with or without pladienolide B

Project description:The purpose was to investigate transcript and splicing changes in U2OS cells following siRNA-mediated depletion of MDC1 and PLRG1 or treatment with the splicing inhibitor pladienolide B. Cells were treated with control siRNA as control condition. Nanopore sequencing of cDNA was performed after library preparation with ONT kits SQK-PCS109 and SQK-PBK004.

2023-01-11 | E-MTAB-12497 | biostudies-arrayexpress

Analysis of global gene expression profiles of A549 cells treated with SETX siRNA under basal conditions

Project description:Untransfected (no siRNA), control siRNA or SETX siRNA treated A549 cells were analyzed for gene expression differences under basal conditions 3 Biological Replicates per condition

2015-03-30 | E-GEOD-52933 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data