Este trabajo fue apoyado por la concesión de los Niños del Discovery Institute MC-II-2006-1 (RDM y TED), el NIH Epigenética Hoja de Ruta de subvención [1R01DA025744-01 y 3R01DA025744 02S1-] (RDM y FLMV), U01AG023746 (SC), el Saigh Fundación (FLMV y TED), 1K08CA140720-01A1 y la limonada de Alex Stand &quot;A&quot; apoyo Premio (TED). Damos las gracias a la Tecnología del Genoma Centro de Acceso en el Departamento de Genética de la Universidad de Washington Escuela de Medicina de la ayuda para el análisis genómico. El Centro está parcialmente financiado por el NCI Cancer Support Center Grant # P30 CA91842 al Centro de Cáncer Siteman y TIC / CTSA Grant # UL1RR024992 de la NationalCenter Recursos para la Investigación (CNRR), un componente de los Institutos Nacionales de Salud (NIH), y NIH Roadmap para la Investigación Médica. Esta publicación es responsabilidad exclusiva de sus autores y no representan necesariamente la opinión oficial de la CNRR o NIH.

<ol>
	<li>Vallania, F. L. M., Druley, T. E., Ramos, E., Wang, J., Borecki, I., Province, M., Mitra, R. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=High-throughput+discovery+of+rare+insertions+and+deletions+in+large+cohorts.">High-throughput discovery of rare insertions and deletions in large cohorts.</a> Genome Research. 20, 1391-1397 (2010).</li><li>Shendure, J., Mitra, R., Varma, C., Church, G. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Advanced+Sequencing+Technologies:+Methods+and+Goals.">Advanced Sequencing Technologies: Methods and Goals.</a> Nature Reviews of Genetics. 5, 335-344 (2004).</li><li>The 1000 Genomes Project Consortium. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+map+of+human+genome+variation+from+population-scale+sequencing.">A map of human genome variation from population-scale sequencing.</a> Nature. 467, 1061-1073 (2010).</li><li>Manolio, T. A., Collins, F. S., Cox, N. J., Goldstein, D. B., Hindorff, L. A., Hunter, D. J., McCarthy, M. I., Ramos, E. M., Cardon, L. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Finding+the+missing+heritability+of+complex+diseases.">Finding the missing heritability of complex diseases.</a> Nature. 461, 747-753 (2009).</li><li>Reich, D. E., Lander, E. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=On+the+allelic+spectrum+of+human+disease.">On the allelic spectrum of human disease.</a> Trends Genet. 17, 502-510 (2001).</li><li>Cohen, J. C., Kiss, R. S., Pertsemlidis, A., Marcel, Y. L., McPherson, R., Hobbs, H. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Multiple+rare+alleles+contribute+to+low+plasma+levels+of+HDL+cholesterol.">Multiple rare alleles contribute to low plasma levels of HDL cholesterol.</a> Science. 305, 869-872 (2004).</li><li>Ji, W., Foo, J. N., O'Roak, B. J., Zhao, H., Larson, M. G., Simon, D. B., Newton-Cheh, C., State, M. W., Levy, D., Lifton, R. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Rare+independent+mutations+in+renal+salt+handling+genes+contribute+to+blood+pressure+variation.">Rare independent mutations in renal salt handling genes contribute to blood pressure variation.</a> Nat. Genet. 40, 592-599 (2008).</li><li>Ahituv, N., Kavaslar, N., Schackwitz, W., Ustaszewska, A., Martin, J., Hebert, S., Doelle, H., Ersoy, B., Kryukov, G., Schmidt, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Medical+sequencing+at+the+extremes+of+human+body+mass.">Medical sequencing at the extremes of human body mass.</a> Am. J. Hum. Genet. 80, 779-791 (2007).</li><li>Druley, T. E., Vallania, F. L., Wegner, D. J., Varley, K. E., Knowles, O. L., Bonds, J. A., Robison, S. W., Doniger, S. W., Hamvas, A., Cole, F. S., Fay, J. C., Mitra, R. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Quantification+of+rare+allelic+variants+from+pooled+genomic+DNA.">Quantification of rare allelic variants from pooled genomic DNA.</a> Nat. Methods. 6, 263-265 (2009).</li><li>Mitra, R. D., Butty, V., Shendure, J., Housman, D., Church, G. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Digital+Genotyping+and+Haplotyping+with+Polymerase+Colonies.">Digital Genotyping and Haplotyping with Polymerase Colonies.</a> Proc. Natl. Acad. Sci. 100, 5926-5931 (2003).</li></ol>

No hay conflictos de interés declarado.

Hay evidencia creciente de que la incidencia y la respuesta terapéutica de los fenotipos comunes, complejos y enfermedades como la obesidad 8, 4 hipercolesterolemia, la hipertensión 7 y otros pueden ser moderadas por perfiles personales de variación poco frecuente. La identificación de los genes y vías donde estos agregados variantes en las poblaciones afectadas tendrán profundas implicaciones diagnósticas y terapéuticas, pero el análisis de las personas afectadas por separado puede llevar mucho tiempo y el costo prohibitivo. Población basada en el análisis ofrece un método más eficiente para investigar la variación genética en múltiples loci. Se presenta un nuevo combinado de ADN protocolo de secuenciación se combina con el paquete de software diseñado para identificar SPLINTER este tipo de variación genética entre las poblaciones. Se demuestra la exactitud de este método en la identificación y cuantificación de los alelos de menor importancia dentro de una gran población combinada de 947 personas, incluyendo las variantes raras que eranllamado de novo a partir de la secuenciación agruparon y validado por pirosecuenciación individuo. Nuestra estrategia principalmente difiere de otros protocolos por la incorporación de un positivo y un control negativo en cada experimento. Esto permite SPLINTER para lograr una precisión mucho mayor y la potencia en comparación con otros enfoques 1. La cobertura óptima de 25-veces por alelo se fija con independencia del tamaño de la piscina, haciendo que el análisis de grandes piscinas practicable que este requisito sólo escalas linealmente con el tamaño de la piscina. Nuestra aproximación es muy flexible y se puede aplicar a cualquier fenotipo de interés, sino también a las muestras que son naturalmente heterogénea, tales como las poblaciones de células mixtas y biopsias tumorales. Dado el interés cada vez mayor en la secuencia combinada de las regiones de destino de gran tamaño como el exoma o genoma, nuestra preparación para la biblioteca y el análisis de SPLINTER es compatible con la costumbre de captura y la secuenciación de todo el exoma, pero la utilidad de alineación en el paquete de SPLINTER no fue diseñado para grandehace referencia a las secuencias. Por lo tanto, hemos utilizado con éxito el alineador de programación dinámica, Novoalign, por todo el genoma alineaciones seguidas por la variante llamada de la muestra conjunta (Ramos et al., Presentado). Por lo tanto, nuestra estrategia combinada de secuenciación se puede ampliar con éxito a las piscinas más grandes con cantidades crecientes de secuencia de destino.

<table border="1"><tbody><tr><td> Reactivo Nombre </td><td> Empresa </td><td> Número de catálogo </td><td> Sección </td></tr><tr><td> PfuUltra de alta fidelidad </td><td> Agilent </td><td> 600384 </td><td> 1.4 </td></tr><tr><td> La betaína </td><td> SIGMA </td><td> B2629 </td><td> 1.4 </td></tr><tr><td> M13mp18 vector de ADN de cadena simple </td><td> NEB </td><td> N4040S </td><td> 1.5 </td></tr><tr><td> pGEM-T Easy </td><td> Promega </td><td> A1360 </td><td> 1.5 </td></tr><tr><td> Polinucleótido quinasa de T4 </td><td> NEB </td><td> M0201S </td><td> 2.2 </td></tr><tr><td> Ligase T4 </td><td> NEB </td><td> M0202S </td><td> 2.2 </td></tr><tr><td> Polietilenglicol 8000 MW </td><td> SIGMA </td><td> P5413 </td><td> 2.2 </td></tr><tr><td> Bioruptor sonicador </td><td> Diagenode </td><td> UCD-200-TS</td><td> 2.3 </td></tr></tbody></table>

detection of rare genomic variants from pooled sequencing using splinter

Como la tecnología de secuenciación del ADN ha avanzado notablemente en los últimos años 2, se ha convertido cada vez más evidente que la cantidad de variación genética entre dos individuos es mayor que antes se pensaba 3. En contraste, la serie basada en la genotipificación no ha identificado una importante contribución de variantes de secuencias comunes a la variabilidad fenotípica de la enfermedad de 4,5 común. En conjunto, estas observaciones han llevado a la evolución de la enfermedad común / variante rara hipótesis que sugiere que la mayoría de la &quot;herencia perdida&quot; en los fenotipos comunes y complejas es más bien debido al perfil personal de un individuo de variantes de ADN raras o privadas 6-8 . Sin embargo, la caracterización de cómo la variación afecta rara fenotipos complejos requiere el análisis de muchos individuos afectados en muchos loci del genoma, y ​​está muy bien en comparación con un estudio similar realizado en una cohorte de afectados. A pesar de la secuenciación de alimentación que ofrecen las plataformas de hoy, unencuesta de población de muchos loci del genoma y el posterior análisis computacional requerido sigue siendo prohibitivo para muchos investigadores. Para satisfacer esta necesidad, hemos desarrollado un enfoque de secuenciación combinado 1,9 y un paquete de software para la detección de una nueva variante de alta precisión poco frecuente de los datos resultantes. La capacidad de los genomas de la piscina de poblaciones enteras de las personas afectadas y de la encuesta el grado de variación genética en varias regiones seleccionadas en una biblioteca de la secuencia única permite un excelente ahorro de costes y tiempo a la metodología tradicional de la secuenciación de una sola muestra. Con una cobertura media por secuenciación del alelo de 25 veces, nuestro algoritmo personalizado, Splinter, utiliza una variante interna de llamar a la estrategia de control para llamar a las inserciones, supresiones y sustituciones hasta cuatro pares de bases de longitud con una alta sensibilidad y especificidad de las piscinas de hasta 1 alelo mutante en 500 individuos. Aquí se describe el método para preparar la s agruparonequencing la biblioteca seguido las instrucciones paso a paso sobre cómo utilizar el paquete para el análisis de la secuenciación SPLINTER combinado ( <a href="http://www.ibridgenetwork.org/wustl/splinter" target="_blank">http://www.ibridgenetwork.org/wustl/splinter</a> ). Se presenta una comparación entre la secuencia combinada de 947 personas, todos los cuales también se sometieron a todo el genoma de matriz, en más de 20kb de la secuenciación por persona. La concordancia entre el genotipado de etiquetado y nuevas variantes de llamadas en el grupo de muestras fueron excelentes. Este método puede ser fácilmente ampliado a cualquier número de loci genómicos y cualquier número de individuos. Mediante la incorporación de los controles internos de amplificación positivas y negativas en proporciones que imitan a la población en estudio, el algoritmo puede ser calibrado para obtener un rendimiento óptimo. Esta estrategia también se puede modificar para su uso con la captura de hibridación o códigos de barras individuales específicos y se puede aplicar a la secuenciación de muestras naturalmente heterogéneos, como el ADN del tumor.

Watch this Scientific Journal Video about Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER at JoVE.com

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

La secuenciación del ADN agrupado es una estrategia rápida y rentable para la detección de variantes raras asociadas con fenotipos complejos en grandes cohortes. A continuación se describe el análisis computacional de combinado, secuenciación de próxima generación de los 32 genes relacionados con el cáncer utilizando el paquete de software Splinter. Este método es escalable y aplicable a cualquier fenotipo de interés.

La detección de raras variantes genómicas de secuenciación agruparon mediante SPLINTER

As DNA sequencing technology has markedly advanced in recent years2, it has become increasingly evident that the amount of genetic variation between any ...

detection-rare-genomic-variants-from-pooled-sequencing-using

Research

JoVE Journal

Biology

15.0K vistas.  Washington University School of Medicine. La secuenciación del ADN agrupado es una estrategia rápida y rentable para la detección de variantes raras asociadas con fenotipos complejos en grandes cohortes. A continuación se describe el análisis computacional de combinado, secuenciación de próxima generación de los 32 genes relacionados con el cáncer utilizando el paquete de software Splinter. Este método es escalable y aplicable a cualquier fenotipo de interés.

Video: Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

Isolation of Genomic DNA from Mouse Tails

El aislamiento de ADN genómico de colas de ratón

Investigación

Biología

Extraction of High Molecular Weight Genomic DNA from Soils and Sediments

The soil microbiome is a vast and relatively unexplored reservoir of genomic diversity and metabolic innovation that is intimately associated with nutrient and energy flow within terrestrial ecosystems. Cultivation-independent environmental genomic, also known as metagenomic, approaches promise unprecedented access to this genetic information with respect to pathway reconstruction and functional screening for high value therapeutic and biomass conversion processes. However, the soil microbiome still remains a challenge largely due to the difficulty in obtaining high molecular weight DNA of sufficient quality for large insert library production. Here we introduce a protocol for extracting high molecular weight, microbial community genomic DNA from soils and sediments. The quality of isolated genomic DNA is ideal for constructing large insert environmental genomic libraries for downstream sequencing and screening applications. 
The procedure starts with cell lysis. Cell walls and membranes of microbes are lysed by both mechanical (grinding) and chemical forces (&beta;-mercaptoethanol). Genomic DNA is then isolated using extraction buffer, chloroform-isoamyl alcohol and isopropyl alcohol. The buffers employed for the lysis and extraction steps include guanidine isothiocyanate and hexadecyltrimethylammonium bromide (CTAB) to preserve the integrity of the high molecular weight genomic DNA. Depending on your downstream application, the isolated genomic DNA can be further purified using cesium chloride (CsCl) gradient ultracentrifugation, which reduces impurities including humic acids. The first procedure, extraction, takes approximately 8 hours, excluding DNA quantification step. The CsCl gradient ultracentrifugation, is a two days process. During the entire procedure, genomic DNA should be treated gently to prevent shearing, avoid severe vortexing, and repetitive harsh pipetting.

A methodology to isolate high molecular weight and high quality genomic DNA from soil microbial community is described.

La extracción de ADN de alta molecular genómico de peso de los suelos y los sedimentos

The soil microbiome is a vast and relatively unexplored reservoir of genomic diversity and metabolic innovation that is intimately associated with ...

Competitive Genomic Screens of Barcoded Yeast Libraries

By virtue of advances in next generation sequencing technologies, we have access to new genome sequences almost daily. The tempo of these advances is accelerating, promising greater depth and breadth. In light of these extraordinary advances, the need for fast, parallel methods to define gene function becomes ever more important. Collections of genome-wide deletion mutants in yeasts and E. coli have served as workhorses for functional characterization of gene function, but this approach is not scalable, current gene-deletion approaches require each of the thousands of genes that comprise a genome to be deleted and verified. Only after this work is complete can we pursue high-throughput phenotyping. Over the past decade, our laboratory has refined a portfolio of competitive, miniaturized, high-throughput genome-wide assays that can be performed in parallel. This parallelization is possible because of the inclusion of DNA 'tags', or 'barcodes,' into each mutant, with the barcode serving as a proxy for the mutation and one can measure the barcode abundance to assess mutant fitness. In this study, we seek to fill the gap between DNA sequence and barcoded mutant collections. To accomplish this we introduce a combined transposon disruption-barcoding approach that opens up parallel barcode assays to newly sequenced, but poorly characterized microbes. To illustrate this approach we present a new Candida albicans barcoded disruption collection and describe how both microarray-based and next generation sequencing-based platforms can be used to collect 10,000 - 1,000,000 gene-gene and drug-gene interactions in a single experiment.

We have developed comprehensive, unbiased genome-wide screens to understand gene-drug and gene-environment interactions. Methods for screening these mutant collections are presented.

Pantallas competitiva Genómica de Bibliotecas de levadura con código de barras

By virtue of advances in next generation sequencing technologies, we have access to new genome sequences almost daily.  The tempo of these advances is ...

Selective Capture of 5-hydroxymethylcytosine from Genomic DNA

5-methylcytosine (5-mC) constitutes ~2-8% of the total cytosines in human genomic DNA and impacts a broad range of biological functions, including gene expression, maintenance of genome integrity, parental imprinting, X-chromosome inactivation, regulation of development, aging, and cancer1. Recently, the presence of an oxidized 5-mC, 5-hydroxymethylcytosine (5-hmC), was discovered in mammalian cells, in particular in embryonic stem (ES) cells and neuronal cells2-4. 5-hmC is generated by oxidation of 5-mC catalyzed by TET family iron (II)/&alpha;-ketoglutarate-dependent dioxygenases2, 3. 5-hmC is proposed to be involved in the maintenance of embryonic stem (mES) cell, normal hematopoiesis and malignancies, and zygote development2, 5-10. To better understand the function of 5-hmC, a reliable and straightforward sequencing system is essential. Traditional bisulfite sequencing cannot distinguish 5-hmC from 5-mC11. To unravel the biology of 5-hmC, we have developed a highly efficient and selective chemical approach to label and capture 5-hmC, taking advantage of a bacteriophage enzyme that adds a glucose moiety to 5-hmC specifically12.
Here we describe a straightforward two-step procedure for selective chemical labeling of 5-hmC. In the first labeling step, 5-hmC in genomic DNA is labeled with a 6-azide-glucose catalyzed by &beta;-GT, a glucosyltransferase from T4 bacteriophage, in a way that transfers the 6-azide-glucose to 5-hmC from the modified cofactor, UDP-6-N3-Glc (6-N3UDPG). In the second step, biotinylation, a disulfide biotin linker is attached to the azide group by click chemistry. Both steps are highly specific and efficient, leading to complete labeling regardless of the abundance of 5-hmC in genomic regions and giving extremely low background. Following biotinylation of 5-hmC, the 5-hmC-containing DNA fragments are then selectively captured using streptavidin beads in a density-independent manner. The resulting 5-hmC-enriched DNA fragments could be used for downstream analyses, including next-generation sequencing.
Our selective labeling and capture protocol confers high sensitivity, applicable to any source of genomic DNA with variable/diverse 5-hmC abundances. Although the main purpose of this protocol is its downstream application (i.e., next-generation sequencing to map out the 5-hmC distribution in genome), it is compatible with single-molecule, real-time SMRT (DNA) sequencing, which is capable of delivering single-base resolution sequencing of 5-hmC.

Described is a two-step labeling process using &beta;-glucosyltransferase (&beta;-GT) to transfer an azide-glucose to 5-hmC, followed by click chemistry to transfer a biotin linker for easy and density-independent enrichment. This efficient and specific labeling method enables enrichment of 5-hmC with extremely low background and high-throughput epigenomic mapping via next-generation sequencing.

Captura selectiva de 5-hidroximetilcitosina a partir de ADN genómico

5-methylcytosine (5-mC) constitutes ~2-8% of the total cytosines in human genomic DNA and impacts a broad range of biological functions, including gene ...

Array Comparative Genomic Hybridization (Array CGH) for Detection of Genomic Copy Number Variants

Array CGH for the detection of genomic copy number variants has replaced G-banded karyotype analysis. This paper describes the technology and its application in a clinical diagnostic service laboratory. DNA extracted from a patient&#8217;s sample (blood, saliva or other tissue types) is labeled with a fluorochrome (either cyanine 5 or cyanine 3). A reference DNA sample is labeled with the opposite fluorochrome. There follows a cleanup step to remove unincorporated nucleotides before the labeled DNAs are mixed and resuspended in a hybridization buffer and applied to an array comprising ~60,000 oligonucleotide probes from loci across the genome, with high probe density in clinically important areas. Following hybridization, the arrays are washed, then scanned and the resulting images are analyzed to measure the red and green fluorescence for each probe. Software is used to assess the quality of each probe measurement, calculate the ratio of red to green fluorescence and detect potential copy number variants.

Array Comparative Genomic Hybridization Array CGH for Detection of Genomic Copy Number Variants

Array CGH for the detection of genomic copy number variants has replaced G-banded karyotype analysis. This paper describes the technology and its application in a diagnostic service laboratory.

Matriz de hibridación genómica comparada (CGH array) para la detección de número de copias genómicas variantes

Array CGH for the detection of genomic copy number variants has replaced G-banded karyotype analysis. This paper describes the technology and its ...

Isolating Potentiated Hsp104 Variants Using Yeast Proteinopathy Models

Many protein-misfolding disorders can be modeled in the budding yeast Saccharomyces cerevisiae. Proteins such as TDP-43 and FUS, implicated in amyotrophic lateral sclerosis, and &#945;-synuclein, implicated in Parkinson&#8217;s disease, are toxic and form cytoplasmic aggregates in yeast. These features recapitulate protein pathologies observed in patients with these disorders. Thus, yeast are an ideal platform for isolating toxicity suppressors from libraries of protein variants. We are interested in applying protein disaggregases to eliminate misfolded toxic protein conformers. Specifically, we are engineering Hsp104, a hexameric AAA+ protein from yeast that is uniquely capable of solubilizing both disordered aggregates and amyloid and returning the proteins to their native conformations. While Hsp104 is highly conserved in eukaryotes and eubacteria, it has no known metazoan homologue. Hsp104 has only limited ability to eliminate disordered aggregates and amyloid fibers implicated in human disease. Thus, we aim to engineer Hsp104 variants to reverse the protein misfolding implicated in neurodegenerative disorders. We have developed methods to screen large libraries of Hsp104 variants for suppression of proteotoxicity in yeast. As yeast are prone to spontaneous nonspecific suppression of toxicity, a two-step screening process has been developed to eliminate false positives. Using these methods, we have identified a series of potentiated Hsp104 variants that potently suppress the toxicity and aggregation of TDP-43, FUS, and &#945;-synuclein. Here, we describe this optimized protocol, which could be adapted to screen libraries constructed using any protein backbone for suppression of toxicity of any protein that is toxic in yeast.

Yeast proteinopathy models are valuable tools to assess the toxicity and aggregation of proteins implicated in disease. Here, we present methods for screening Hsp104 variant libraries for toxicity suppressors. This protocol could be adapted to screen any protein library for toxicity suppressors of any protein that is toxic in yeast.

Aislar Potenciada Hsp104 Variantes Usando levadura Modelos proteinopatía

Many protein-misfolding disorders can be modeled in the budding yeast Saccharomyces cerevisiae. Proteins such as TDP-43 and FUS, implicated in amyotrophic ...

TRAP-rc, Translating Ribosome Affinity Purification from Rare Cell Populations of Drosophila Embryos

Measuring levels of mRNAs in the process of translation in individual cells provides information on the proteins involved in cellular functions at a given point in time. The protocol dubbed Translating Ribosome Affinity Purification (TRAP) is able to capture this mRNA translation process in a cell-type-specific manner. Based on the affinity purification of polysomes carrying a tagged ribosomal subunit, TRAP can be applied to translatome analyses in individual cells, making it possible to compare cell types during the course of developmental processes or to track disease development progress and the impact of potential therapies at molecular level. Here we report an optimized version of the TRAP protocol, called TRAP-rc (rare cells), dedicated to identifying engaged-in-translation RNAs from rare cell populations. TRAP-rc was validated using the Gal4/UAS targeting system in a restricted population of muscle cells in Drosophila embryos. This novel protocol allows the recovery of cell-type-specific RNA in sufficient quantities for global gene expression analytics such as microarrays or RNA-seq. The robustness of the protocol and the large collections of Gal4 drivers make TRAP-rc a highly versatile approach with potential applications in cell-specific genome-wide studies.

TRAP-rc, Translating Ribosome Affinity Purification from Rare Cell Populations of Drosophila Embryos

Translating Ribosome Affinity Purification (TRAP) is able to capture cell-type-specific translation of mRNA. Here we report the first TRAP protocol dedicated to isolation of mRNA in rare cell populations of Drosophila embryos.

TRAP-rc, Traducción ribosoma Affinity Purificación de poblaciones de células raras de<em&gt; Drosophila</em&gt; Los embriones

Measuring levels of mRNAs in the process of translation in individual cells provides information on the proteins involved in cellular functions at a given ...

Amplification, Next-generation Sequencing, and Genomic DNA Mapping of Retroviral Integration Sites

Retroviruses exhibit signature integration preferences on both the local and global scales. Here, we present a detailed protocol for (1) generation of diverse libraries of retroviral integration sites using ligation-mediated PCR (LM-PCR) amplification and next-generation sequencing (NGS), (2) mapping the genomic location of each virus-host junction using BEDTools, and (3) analyzing the data for statistical relevance. Genomic DNA extracted from infected cells is fragmented by digestion with restriction enzymes or by sonication. After suitable DNA end-repair, double-stranded linkers are ligated onto the DNA ends, and semi-nested PCR is conducted using primers complementary to both the long terminal repeat (LTR) end of the virus and the ligated linker DNA. The PCR primers carry sequences required for DNA clustering during NGS, negating the requirement for separate adapter ligation. Quality control (QC) is conducted to assess DNA fragment size distribution and adapter DNA incorporation prior to NGS. Sequence output files are filtered for LTR-containing reads, and the sequences defining the LTR and the linker are cropped away. Trimmed host cell sequences are mapped to a reference genome using BLAT and are filtered for minimally 97% identity to a unique point in the reference genome. Unique integration sites are scrutinized for adjacent nucleotide (nt) sequence and distribution relative to various genomic features. Using this protocol, integration site libraries of high complexity can be constructed from genomic DNA in three days. The entire protocol that encompasses exogenous viral infection of susceptible tissue culture cells to integration site analysis can therefore be conducted in approximately one to two weeks. Recent applications of this technology pertain to longitudinal analysis of integration sites from HIV-infected patients.

We describe a protocol for amplifying retroviral integration sites from the genomic DNA of infected cells, sequencing the amplified virus-host junctions, and then mapping these sequences to a reference genome. We also describe techniques to quantify the distribution of integration sites relative to various genomic annotations using BEDTools.

Amplificación, secuenciación de próxima generación, y Genómica Mapeo de ADN retrovirales sitios de integración

Retroviruses exhibit signature integration preferences on both the local and global scales. Here, we present a detailed protocol for (1) generation of ...

Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations

RNA sequencing (RNAseq) is a versatile method that can be utilized to detect and characterize gene expression, mutations, gene fusions, and noncoding RNAs. Standard RNAseq requires 30 - 100 million sequencing reads and can include multiple RNA products such as mRNA and noncoding RNAs. We demonstrate how targeted RNAseq (capture) permits a focused study on selected RNA products using a desktop sequencer. RNAseq capture can characterize unannotated, low, or transiently expressed transcripts that may otherwise be missed using traditional RNAseq methods. Here we describe the extraction of RNA from cell lines, ribosomal RNA depletion, cDNA synthesis, preparation of barcoded libraries, hybridization and capture of targeted transcripts and multiplex sequencing on a desktop sequencer. We also outline the computational analysis pipeline, which includes quality control assessment, alignment, fusion detection, gene expression quantification and identification of single nucleotide variants. This assay allows for targeted transcript sequencing to characterize gene expression, gene fusions, and mutations.

We describe a targeted RNA sequencing-based method that includes preparation of indexed cDNA libraries, hybridization and capture with custom probes and data analysis to interrogate selected transcripts for gene expression, mutations, and gene fusions. Targeted RNAseq permits cost-effective, rapid evaluation of selected transcripts on a desktop sequencer.

La secuenciación de ARN dirigidos Ensayo para caracterizar la expresión génica y la genómica alteraciones

RNA sequencing (RNAseq) is a versatile method that can be utilized to detect and characterize gene expression, mutations, gene fusions, and noncoding ...

Genome Engineering of Primary Human B Cells Using CRISPR/Cas9

B cells are lymphocytes derived from hematopoietic stem cells and are a key component of the humoral arm of the adaptive immune system. They make attractive candidates for cell-based therapies because of their ease of isolation from peripheral blood, their ability to expand in vitro, and their longevity in vivo. Additionally, their normal biological function&#8212;to produce large amounts of antibodies&#8212;can be utilized to express very large amounts of a therapeutic protein, such as a recombinant antibody to fight infection, or an enzyme for the treatment of enzymopathies. Here, we provide detailed methods for isolating primary human B cells from peripheral blood mononuclear cells (PBMCs) and activating/expanding isolated B cells in vitro. We then demonstrate the steps involved in using the CRISPR/Cas9 system for site-specific KO of endogenous genes in B cells. This method allows for efficient KO of various genes, which can be used to study the biological functions of genes of interest. We then demonstrate the steps for using the CRISPR/Cas9 system together with a recombinant, adeno-associated, viral (rAAV) vector for efficient site-specific integration of a transgene expression cassette in B cells. Together, this protocol provides a step-by-step engineering platform that can be used in primary human B cells to study biological functions of genes as well as for the development of B-cell therapeutics.

Here we provide a detailed, step-by-step protocol for CRISPR/Cas9-based genome engineering of primary human B cells for gene knockout (KO) and knock-in (KI) to study biological functions of genes in B cells and the development of B-cell therapeutics.