![]() Fluorescence in situ hybridization (FISH) with rRNA-targeted oligonucleotide probes. Dynamics and spatial genomics of the nascent transcriptome by intron seqFISH. Spatially resolved, highly multiplexed RNA profiling in single cells. Single-chromosome transcriptional profiling reveals chromosomal gene expression regulation. Integrated spatial genomics reveals global architecture of single nuclei. Genome-scale imaging of the 3D organization and transcriptional activity of chromatin. Visualizing DNA folding and RNA in embryos at single-cell resolution. Microscopy-based chromosome conformation capture enables simultaneous visualization of genome organization and transcription in intact organisms. Super-resolution chromatin tracing reveals domains and cooperative interactions in single cells. Spatial organization of chromatin domains and compartments in single chromosomes. ![]() Versatile design and synthesis platform for visualizing genomes with Oligopaint FISH probes. Fluorescence in situ hybridization with high-complexity repeat-free oligonucleotide probes generated by massively parallel synthesis. Visualization of fine-scale genomic structure by oligonucleotide-based high-resolution FISH. Large-scale de novo DNA synthesis: technologies and applications. Imaging individual mRNA molecules using multiple singly labeled probes. Visualization of single RNA transcripts in situ. Simultaneous detection of different mRNA sequences coding for neuropeptide hormones by double in situ hybridization using FITC- and biotin-labeled oligonucleotides. Perturbation of nuclear architecture by long-distance chromosome interactions. Oligonucleotide probes for the analysis of specific repetitive dna sequences by fluorescence in situ hybridization. A highly conserved repetitive DNA sequence, (TTAGGG)(n), present at the telomeres of human chromosomes. Immunological methods for mapping genes on Drosophila polytene chromosomes. A new method for fluorescence microscopical localization of specific DNA sequences by in situ hybridization of fluorochrome-labelled RNA. High resolution detection of DNA-RNA hybrids in situ by indirect immunofluorescence. Molecular hybridization of radioactive DNA to the DNA of cytological preparations. Raw and processed microscopy images are available upon request. All repositories are available under the MIT license. All genome-scale probe collections, primer sequences, bridge sequences, SABER-associated sequences, and transcriptome intersects hosted on paintshop.io are available to download from repository. The chicken galGal6 genome assembly was downloaded from. The chicken galGal5 genome assembly was downloaded from. The rat rn6 genome assembly was downloaded from. cerevisiae sacCer3 genome assembly was downloaded from. ![]() thaliana TAIR10 genome assembly was downloaded from. The zebrafish danRer11 genome assembly was downloaded from. melanogaster dm6 genome assembly was downloaded from. ![]() elegans ce11 genome assembly was downloaded from. The mouse mm10 genome assembly was downloaded from. The mouse mm9 genome assembly was downloaded from. ![]() The human hg38 genome assembly was downloaded from. The human hg19 genome assembly was downloaded from. The original ‘Full 40-mer’ iFISH4u hg19 genome-scale probe collection was downloaded from. The original OligoMiner hg38 ‘balance’ genome-scale probe collection was downloaded from. The original OligoMiner hg19 ‘balance’ genome-scale probe collection was downloaded from. The original ‘OligoPaints 2012 hg19’ genome-scale probe collection was downloaded from. PaintSHOP democratizes and standardizes the process of designing complex probe sets for the oligo FISH community. PaintSHOP enables researchers to identify probes for their experimental targets efficiently, to incorporate additional necessary sequences such as primer pairs and to easily generate files documenting library design. Here, we introduce paint server and homology optimization pipeline (PaintSHOP), an interactive platform for the design of oligo FISH experiments. However, there are few existing computational tools to support the bioinformatics workflows necessary to carry out these experiments using oligo FISH probes. Recently, considerable progress has been made in developing oligonucleotide (oligo)-based FISH methods that have enabled researchers to study the three-dimensional organization of the genome at super-resolution and visualize the spatial patterns of gene expression for thousands of genes in individual cells. Fluorescence in situ hybridization (FISH) allows researchers to visualize the spatial position and quantity of nucleic acids in fixed samples. ![]()
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