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Scheiman, Jonathan

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Scheiman

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Jonathan

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Scheiman, Jonathan

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2014 - 20153

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Author's Publications: search.filters.isAuthorOfPublication.59b5d36c-1653-4d7b-9361-63a38ea35e3e

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Now showing 1 - 3 of 3
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    Highly-efficient Cas9-mediated transcriptional programming
    (2015) Chavez, Alejandro; Scheiman, Jonathan; Vora, Suhani; Pruitt, Benjamin W.; Tuttle, M; Iyer, Eswar; Lin, Shuailiang; Kiani, Samira; Guzman, Christopher D.; Wiegand, Daniel; Ter-Ovanesyan, Dmitry; Braff, Jonathan L.; Davidsohn, Noah; Housden, Benjamin E; Perrimon, Norbert; Weiss, Ron; Aach, John; Collins, James; Church, George
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    Highly Multiplexed Subcellular RNA Sequencing in Situ
    (American Association for the Advancement of Science, 2014-03-21) Lee, Je Hyuk; Daugharthy, Evan; Scheiman, Jonathan; Kalhor, Reza; Ferrante, Thomas; Yang, Joyce; Terry, Richard; Jeanty, Sauveur; Li, Chao; Amamoto, Ryoji; Peters, Derek; Turczyk, Brian; Marblestone, Adam; Inverso, Samuel; Bernard, Amy; Mali, Prashant; Rios, Xavier; Aach, John; Church, George
    Understanding the spatial organization of gene expression with single nucleotide resolution requires localizing the sequences of expressed RNA transcripts within a cell in situ. Here we describe fluorescent in situ RNA sequencing (FISSEQ), in which stably cross-linked cDNA amplicons are sequenced within a biological sample. Using 30-base reads from 8,742 genes in situ, we examined RNA expression and localization in human primary fibroblasts using a simulated wound healing assay. FISSEQ is compatible with tissue sections and whole mount embryos, and reduces the limitations of optical resolution and noisy signals on single molecule detection. Our platform enables massively parallel detection of genetic elements, including gene transcripts and molecular barcodes, and can be used to investigate cellular phenotype, gene regulation, and environment in situ.
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    Fluorescent in situ sequencing (FISSEQ) of RNA for gene expression profiling in intact cells and tissues
    (Springer Nature, 2015) Lee, Je Hyuk; Daugharthy, Evan R; Scheiman, Jonathan; Kalhor, Reza; Ferrante, Thomas; Terry, Richard; Turczyk, Brian M; Yang, Joyce L; Lee, Ho Suk; Aach, John; Zhang, Kun; Church, George
    RNA sequencing measures the quantitative change in gene expression over the whole transcriptome, but it lacks spatial context. On the other hand, in situ hybridization provides the location of gene expression, but only for a small number of genes. Here we detail a protocol for genome-wide profiling of gene expression in situ in fixed cells and tissues, in which RNA is converted into cross-linked cDNA amplicons and sequenced manually on a confocal microscope. Unlike traditional RNA-seq our method enriches for context-specific transcripts over house-keeping and/or structural RNA, and it preserves the tissue architecture for RNA localization studies. Our protocol is written for researchers experienced in cell microscopy with minimal computing skills. Library construction and sequencing can be completed within 14 d, with image analysis requiring an additional 2 d.