Project description:SELEX (systematic evolution of ligands by exponential enrichment) and RNA Immunoprecipitation (RIP)-seq revealed that CIRBP directly binds the 3’UTR of Atp5g3.
Project description:SELEX (systematic evolution of ligands by exponential enrichment), chromatin immunoprecipitation (ChIP)-seq, and crosslinking immunoprecipitation (CLIP)-seq showed that the DDX43 KH domain binds C/T rich DNA and U rich RNA.
Project description:We performed an unsupervised, high-throughput (HT) sequencing-cell SELEX (systematic evolution of ligands by exponential enrichment) using the MDSC-derived cell line MSC2. Specifically untreated MSC2 and IL4 treated MSC2 were used as negative and positive selector respectively. Selection was started from a 5 ug of 40bp variable region linked to two constant region.
Project description:We performed a high-throughput systematic evolution of ligands by exponential enrichment (HT-SELEX) approach on all 371 annotated TFs in P. aeruginosa. This study provides a valuable resource for TF binding specificities in P. aeruginosa and demonstrates a novel and an integrative analysis for seeking the virulence-associated TFs and its target genes.
Project description:Type 1 Diabetes is still an incurable disease characterized by autoimmune destruction of insulin-producing beta cells within the islet of Langerhans in the pancreas. Currently, there are no methods to monitor beta-cell mass in humans or deliver therapeutics specifically to beta cells. Here we performed Cluster Systematic Evolution of Ligands by Exponential Enrichment (SELEX) experiments and toggle SELEX experiments to identify RNA aptamers specific for human islets. In the cluster SELEX, we started from a random library of RNA nucleotides composed of a 40 nucleotide long variable region flanked by two constant regions. We performed eight selection cycles using hand-picked islets and islet-depleted acinar tissue from 4 cadaveric human donors as positive and negative selectors. In the toggle SELEX, we conducted eight cycles of selection using islets and acinar tissue from mice, followed by two cycles of selection using human tissues. The polyclonal libraries from the two selection strategies showed a convergent evolution of ligands and increased specificity for human islets.
Project description:The ability to detect and target β cells in vivo can drastically refine the way diabetes is studied and treated. By an unsupervised Systematic evolution of ligands by exponential enrichment (SELEX) we identified two RNA aptamers that specifically recognize mouse and human β cells in vitro and in vivo. Here we took advantage of commercially available high density protein arrays to identify putative target of the two islet specific aptamers. Briefly, 5' biotynilated RNA aptamer 1-717 and m12-3773 were chemically produced , complexed with Alexafluor 647-streptavidin and used as probe on the HuProt™ v2.0 19K protein array. Putative binders were further confirmed by cold target inhibition assays, silencing experiments, and surface plasmon resonance.
