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TranscriptomicsTranscriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP: sequencing data
We applied 4-thiouridine to cultured cells expressing the FLAG/HA-tagged RNA-binding proteins (RBPs) followed by UV 365 nm irradiation. The crosslinked RNA-protein complexes were isolated by immunoprecipitation, and the covalently bound RNA was partially digested with RNase T1 and radiolabeled. The ...
ORGANISM(S): Homo sapiens 
2010-05-21 | E-GEOD-21918 | biostudies-arrayexpress
TranscriptomicsTranscriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP
This SuperSeries is composed of the following subset Series: GSE21574: Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP: QKI data GSE21575: Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP: IGF2BP data GSE215...
ORGANISM(S): Homo sapiens 
2010-04-29 | E-GEOD-21578 | biostudies-arrayexpress
TranscriptomicsThe Drosophila immune response towards entomopathogenic nematodes and their associated bacteria.
Entomopathogenic nematodes (EPNs) of the genera Heterorhabditis are obligate and lethal insect parasites. In recent years they have been used increasingly as biological control agents. These EPNs are symbiotically associated with bacteria of the genera Photorhabdus. The bacterial symbionts are essen...
ORGANISM(S): Drosophila melanogaster 
2014-03-07 | E-MTAB-1542 | biostudies-arrayexpress
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
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
ProteomicsLongitudinal study of the small urinary extracellular vesicle proteome during living donor kidney transplantation
Urine was obtained from healthy kidney donors, from transplanted kidneys intrasurgery, at postoperative day 1 and at later timepoints. Exosomes were isolated and measured using nLC-MS/MS. For details, see the accompanying manuscript.
ORGANISM(S): Homo sapiens (Human) 
2021-08-30 | PXD005219 | Pride
Exosomes Transplantation Urine Human Kidney 
TranscriptomicsComprehensive array CGH of normal karyotype Myelodysplastic syndrome reveals hidden recurrent and individual genomic copy number aberrations with prognostic relevance
About 40% of patients with myelodysplastic syndromes (MDS) present with a normal karyotype and they are facing different courses of disease. To advance the biological understanding and find molecular prognostic markers we performed a high resolution oligonucleotide array study of 107 MDS patients (F...
ORGANISM(S): Homo sapiens 
2011-01-30 | E-GEOD-24602 | biostudies-arrayexpress
TranscriptomicsMutated KRAS induces overexpression of DUSP4, a MAP-kinase phosphatase, and SMYD3, a histone methyltransferase, in rectal carcinomas
Mutations of the KRAS oncogene are predictive for resistance to treatment with antibodies against the epithelial growth factor receptor in patients with colorectal cancer. Overcoming this therapeutic dilemma could potentially be achieved by the introduction of drugs that inhibit signaling pathways t...
ORGANISM(S): Homo sapiens 
2011-03-11 | E-GEOD-20842 | biostudies-arrayexpress
TranscriptomicsGene expression profiling in AML with normal karyotype: A multicenter study investigating molecular markers in 251 cases
Acute myeloid leukemia (AML) is a heterogeneous disease and AML with normal karyotype (AML-NK) is categorized as an intermediate-risk group. Over the past years molecular analyses successfully identified biomarkers that will further allow to dissecting clinically meaningful subgroups in this disease...
ORGANISM(S): Homo sapiens 
2009-12-31 | E-GEOD-15434 | biostudies-arrayexpress
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