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TranscriptomicsTranscriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP: IGF2BP data
To test the influence of IGF2BPs on the stability of their interacting mRNAs, as reported previously for some targets (Yisraeli, 2005), we simultaneously depleted all three IGF2BP family members using siRNAs and compared the cellular RNA from knockdown and mock-transfected cells on microarrays. The ...
ORGANISM(S): Homo sapiens 
2010-05-27 | E-GEOD-21575 | biostudies-arrayexpress
TranscriptomicsGlobal Target mRNA Specification and Regulation by RNA-Binding Protein ZFP36/Tristetraprolin/TTP [PAR-CLIP]
Tristetraprolin/ZFP36/TTP and ELAVL1/HuR are two disease-relevant RNA-binding proteins (RBPs) that both interact with AU-rich sequences but have antagonistic roles. While ELAVL1 binding has been profiled in several studies, the precise in vivo binding specificity of ZFP36 has not been investigated o...
ORGANISM(S): Homo sapiens 
2013-12-24 | E-GEOD-53184 | biostudies-arrayexpress
TranscriptomicsTranscriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP: QKI data
To assess whether the transcripts identified by PAR-CLIP are regulated by the RNA-binding protein (RBP) Quaking (QKI), we analyzed the mRNA levels of mock-transfected and QKI-specific siRNA-transfected cells with microarrays. Transcripts crosslinked to QKI were significantly upregulated upon siRNA t...
ORGANISM(S): Homo sapiens 
2010-05-27 | E-GEOD-21574 | biostudies-arrayexpress
TranscriptomicsTranscriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP: miRNA inhibition data
To obtain evidence that Argonaute (AGO) crosslink-centered regions (CCRs) indeed contain functional miRNA-binding sites, we blocked 25 of the most abundant miRNAs in HEK 293 cells (Figure 5C of PMID 20371350) by transfection of a cocktail of 2'-O-methyl-modified antisense oligoribonucleotides and mo...
ORGANISM(S): Homo sapiens 
2010-05-27 | E-GEOD-21577 | biostudies-arrayexpress
TranscriptomicssiRNA profiling of HeLa cells reveals strand-specific 5-O-methylation of siRNA duplexes controls guide strand selection and targeting specificity.
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 miR...
ORGANISM(S): Homo sapiens 
2008-06-11 | E-GEOD-10960 | biostudies-arrayexpress
TranscriptomicsMulticolor miRNA fluorescence in situ hybridization for tumor differential diagnosis
We profiled and quantitated miRNAs in two skin tumors (Basal cell carcinoma and Merkel cell carcinoma) and identified tumor-specific miRNAs. We used these tumor-specific miRNAs to guide development of miRNA fluorescence in situ hybridization. 2 barcoded sequencing runs, including 40 unique samples (...
ORGANISM(S): Homo sapiens 
2013-06-28 | E-GEOD-34137 | biostudies-arrayexpress
TranscriptomicsMicroRNA sequence and expression analysis in breast tumors by deep sequencing [miRNA sequence data]
MicroRNAs (miRNAs) regulate many genes critical for tumorigenesis. We profiled miRNAs from 11 normal breast tissues, 17 non-invasive, 151 invasive breast carcinomas, and 6 cell lines by in-house-developed barcoded Solexa sequencing. miRNAs were organized in genomic clusters representing promoter-con...
ORGANISM(S): Homo sapiens 
2011-06-06 | E-GEOD-29173 | biostudies-arrayexpress
TranscriptomicsMicroRNA sequence and expression analysis in breast tumors by deep sequencing
This SuperSeries is composed of the following subset Series: GSE29173: MicroRNA sequence and expression analysis in breast tumors by deep sequencing [miRNA sequence data] GSE29174: MicroRNA sequence and expression analysis in breast tumors by deep sequencing [mRNA expression array data] MicroRNAs (m...
ORGANISM(S): Homo sapiens 
2011-06-07 | E-GEOD-28884 | biostudies-arrayexpress
TranscriptomicsIdentification of mRNAs bound and regulated by human LIN28 proteins and molecular requirements for RNA recognition [RNA-Seq]
Human LIN28A and B are RNA-binding proteins (RBPs) conserved in animals with important roles during development and stem cell reprogramming. We used Photoactivatable-Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation (PAR-CLIP) in HEK293 cells and identified a largely overlapping set of ~3...
ORGANISM(S): Homo sapiens 
2013-02-26 | E-GEOD-44568 | biostudies-arrayexpress
TranscriptomicsIdentification of mRNAs bound and regulated by human LIN28 proteins and molecular requirements for RNA recognition [PAR-CLIP]
Human LIN28A and B are RNA-binding proteins (RBPs) conserved in animals with important roles during development and stem cell reprogramming. We used Photoactivatable-Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation (PAR-CLIP) in HEK293 cells and identified a largely overlapping set of ~3...
ORGANISM(S): Homo sapiens 
2013-02-26 | E-GEOD-44615 | biostudies-arrayexpress
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