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TranscriptomicsProbing the off-target effect of EGFP siRNA and pro-siRNA in the HeLa-d1EGFP cell line
We have develped a novel method of making siRNAs (named pro-siRNA for prokaryotic siRNA). To evaluate off-targeting of pro-siRNA, we compared the mRNA expression profiles of HeLa-d1EGFP cells transfected with 4 nM EGFP siRNAs and pro-siRNAs by microarray. We used microarray to study the off-target e...
ORGANISM(S): Homo sapiens 
2013-02-12 | E-GEOD-44256 | biostudies-arrayexpress
Transcriptomicshuman hTERT-RPE1 cell spheroid : Control siRNA transfected vs. YAP1 siRNA transfected
Transcriptional profiling of human hTERT-RPE1 cell spheroids comparing Control siRNA transfected hTERT-RPE1 cell spheroids with those transfected with YAP1 siRNA. Two-condition experiment, Control siRNA vs.YAP1 siRNA hTERT-RPE1 cell spheroids. Biological replicates: 1 Control siRNA, 1YAP1 siRNA tran...
ORGANISM(S): Homo sapiens 
2015-02-01 | E-GEOD-54146 | biostudies-arrayexpress
TranscriptomicsLentiviral shRNA library screen to identify growth-related genes in malignant melanoma
Little is known about genes that promote melanoma cell growth and proliferation. siRNAs may be used to address the role of individual genesin these processes. RNAi library screens were used in the past to gain a comprehensive overview of all genes involved in cell growth, proliferation, migration an...
ORGANISM(S): Homo sapiens 
2014-01-24 | E-GEOD-46675 | biostudies-arrayexpress
TranscriptomicsLNCaP cells: shRNA library with bicalutamide
Short hairpin RNA library-based functional screening identified ribosomal protein L31 that modulates prostate cancer cell growth Vehicle vs. bicalutamide treated LNCaP cells infected with lentiviral shRNA library. Biological replicates: 2 vehicle treatments, 2 bicalutamide treatments.
ORGANISM(S): Homo sapiens 
2015-05-15 | E-GEOD-60382 | biostudies-arrayexpress
TranscriptomicsAnalysis of 22G siRNA triggered siRNA amplification in Caenorhabditis elegans
To determine if an endogenous 22G siRNA sensor transgene is subject to siRNA amplification, small RNAs were deep sequenced from the sensor and from a control transgene that is identical to the sensor but lacks an siRNA target site. Small RNAs were isolated from synchronized young adult C. elegans an...
ORGANISM(S): Caenorhabditis elegans 
2011-12-10 | E-GEOD-34320 | biostudies-arrayexpress
TranscriptomicsNanopore RNA-seq of human osteosarcoma cell line U2OS treated with siRNA against MDC1, PLRG1, or control siRNA with or without pladienolide B
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 libra...
ORGANISM(S): Homo sapiens 
2023-01-11 | E-MTAB-12497 | biostudies-arrayexpress
TranscriptomicsDetection of Pol IV-dependent transcripts at the genomic scale in Arabidopsis reveals features and regulation of siRNA biogenesis
24 nucleotide siRNAs are central players in RNA-directed DNA methylation (RdDM), a process that establishes DNA methylation at transposable elements to ensure genome stability. The plant-specific RNA polymerase IV (Pol IV) is required for siRNA biogenesis and is thought to transcribe RdDM loci to pr...
ORGANISM(S): Arabidopsis thaliana 
2014-11-11 | E-GEOD-57215 | biostudies-arrayexpress
Proteomicsrole of LIN28B protein in medulloblastoma by siRNA-mediated silencing of LIN28B in Daoy cells
To understand the role of LIN28B protein in medulloblastoma by siRNA-mediated silencing of LIN28B in Daoy cells and analysing the differentially-regulated proteins and pathways.
ORGANISM(S): Homo sapiens (Human) 
2025-05-06 | PXD022481 | Pride
Medulloblastoma Sirna Lin28b 
TranscriptomicsRNA sequencing (RNA-SEQ) of EPAS1 knockdown by siRNA in endothelial cells
Purpose: By integrating DNA methylation and gene expression of COPD lung tissues, we identified EPAS1 as a key regulator whose downstream genes significantly overlapped with multiple genes sets associated with COPD disease severity. EPAS1 is distinct in comparison with other key regulators in terms ...
ORGANISM(S): Homo sapiens 
2015-01-16 | E-GEOD-62974 | biostudies-arrayexpress
TranscriptomicsAnalysis of 22G siRNA triggered siRNA amplification and 3' 2'-O-methylated small RNAs in Caenorhabditis elegans
Small RNAs, including piRNAs, miRNAs and endogenous siRNAs, bind Argonaute proteins to form RNA-silencing complexes that target coding genes, transposons and aberrant RNAs. To assess the requirements for endogenous siRNA formation and activity in C. elegans, we developed a GFP-based sensor for the e...
ORGANISM(S): Caenorhabditis elegans 
2012-02-03 | E-GEOD-35550 | biostudies-arrayexpress
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