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- 1From: Nature Protocols. (Vol. 6, Issue 12) Peer-ReviewedHere we describe a protocol for generating 3D human intestinal tissues (called organoids) in vitro from human pluripotent stem cells (hPsCs). To generate intestinal organoids, pluripotent stem cells are first...
- 2From: Nature Protocols. (Vol. 6, Issue 12) Peer-ReviewedThis protocol and the accompanying software program called LEVER (lineage editing and validation) enable quantitative automated analysis of phase-contrast time-lapse images of cultured neural stem cells. Images are...
- 3From: Nature Protocols. (Vol. 6, Issue 12) Peer-ReviewedEnvironment-sensitive fluorophores have different quantum yields in different solvents. 6-Dimethylaminonaphthalimide (6-DMN), for example, has a low quantum yield in aqueous solutions, but is highly fluorescent in...
- 4From: Nature Protocols. (Vol. 6, Issue 12) Peer-ReviewedConfocal live imaging is a key tool for studying cell behavior in the whole zebrafish embryo. Here we provide a detailed protocol that is adaptable for imaging any progenitor cell behavior in live zebrafish embryos. As...
- 5From: Nature Protocols. (Vol. 6, Issue 12) Peer-Reviewed
Design and self-assembly of siRNA-functionalized RNA nanoparticles for use in automated nanomedicine
Individual genes can be targeted with siRNAs. The use of nucleic acid nanoparticles (NPs) is a convenient method for delivering combinations of specific siRNAs in an organized and programmable manner. We present three... - 6From: Nature Protocols. (Vol. 6, Issue 12) Peer-ReviewedThe unprecedented increase in the throughput of DNA sequencing driven by next-generation technologies now allows efficient analysis of the complete protein-coding regions of genomes (exomes) for multiple samples in a...
- 7From: Nature Protocols. (Vol. 6, Issue 12) Peer-ReviewedWe have recently shown that a fraction of the total cellular pool of the small GTPase RhoA resides in the nucleus, and that the nuclear guanine nucleotide exchange factor (GEF) Net1 has a role in the regulation of its...
- 8From: Nature Protocols. (Vol. 6, Issue 12) Peer-ReviewedA comprehensive understanding of the cell biology of adult neural stem cells (aNSCs) requires direct observation of aNSC division and lineage progression in the absence of niche-dependent signals. Here we describe a...
- 9From: Nature Protocols. (Vol. 6, Issue 12) Peer-ReviewedThis protocol outlines a procedure for collecting and analyzing point spread functions (PSFs). It describes how to prepare fluorescent microsphere samples, set up a confocal microscope to properly collect 3D confocal...
- 10From: Nature Protocols. (Vol. 6, Issue 12) Peer-ReviewedFluorescence resonance energy transfer (FRET)-based molecular biosensors serve as important tools for studying protein activity in live cells and have been widely used for this purpose over the past decade. However,...
- 11From: Nature Protocols. (Vol. 6, Issue 12) Peer-ReviewedThe unprecedented increase in the throughput of DNA sequencing driven by next-generation technologies now allows efficient analysis of the complete protein-coding regions of genomes (exomes) for multiple samples in a...
- 12From: Nature Protocols. (Vol. 6, Issue 12) Peer-ReviewedThis protocol describes a method for determining both the average number and variance of proteins, in the few to tens of copies, in isolated cellular compartments such as organelles and protein complexes. Other...
- 13From: Nature Protocols. (Vol. 6, Issue 12) Peer-ReviewedMicroRNAs (miRNAs) regulate gene expression by pairing with complementary sequences in the 3' untranslated regions (UTRs) of transcripts. Although the molecular mechanism underlying miRNA biogenesis and activity is...
- 14From: Nature Protocols. (Vol. 6, Issue 12) Peer-ReviewedThe transcription factor affinity prediction (TRAP) method calculates the affinity of transcription factors for DNA sequences on the basis of a biophysical model. This method has proven to be useful for several...
- 15From: Nature Protocols. (Vol. 6, Issue 12) Peer-ReviewedNeural stem cells (NSCs) have the remarkable capacity to self-renew and the lifelong ability to generate neurons in the adult mammalian brain. However, the molecular and cellular mechanisms contributing to these...
- 16From: Nature Protocols. (Vol. 6, Issue 12) Peer-ReviewedIn this protocol, we describe the imaging of single axons in the rat optic nerve in vivo. Axons are labeled through the intravitreal injection of adeno-associated viral vectors (AAVs) expressing a fluorophore (duration...
- 17From: Nature Protocols. (Vol. 6, Issue 12) Peer-Reviewed
Chromatin immunoprecipitation and high-throughput sequencing from paraffin-embedded pathology tissue
Formalin-fixed, paraffin-embedded (FFPE) samples represent the gold standard for storage of pathology samples. Here we describe pathology tissue chromatin immunoprecipitation (PAT-ChIP), a technique for extraction and... - 18From: Nature Protocols. (Vol. 6, Issue 12) Peer-ReviewedInsertion sequencing (INSeq) is a method for determining the insertion site and relative abundance of large numbers of transposon mutants in a mixed population of isogenic mutants of a sequenced microbial species. INSeq...