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    Adapting the Smart-seq2 Protocol for Robust Single Worm RNA-seq
    [Abstract] Most nematodes are small worms that lack enough RNA for regular RNA-seq protocols without pooling hundred to thousand of individuals. We have adapted the Smart-seq2 protocol in order to sequence the transcriptome of an individual worm. While developed for individual Steinernema carpocapsae and Caenorhabditis elegans larvae as ...
    Preparation of Multiplexed Small RNA Libraries from Plants
    [Abstract] High-throughput sequencing is a powerful tool for exploring small RNA populations in plants. The ever-increasing output from an Illumina Sequencing System allows for multiplexing multiple samples while still obtaining sufficient data for small RNA discovery and characterization. Here we describe a protocol for generating multiplexed small RNA ...
    Mapping and Analysis of Illumina Reads for Transcriptome of Medicago Truncatula During the Early Organogenesis of the Nodule
    [Abstract] Medicago truncatula serves as a model plant for legume genetics and genomics. We used RNA-Seq to characterize the transcriptome during the early organogenesis of the nodule and during its functioning. We generated approximately 135.5 million high-quality 36-bp reads, which were then aligned with the M. truncatula genome sequence ...
    RNA-Seq Library Generation from Rare Human Cells Isolated by FACS
    Authors:  Sofia Gkountela and Amander T. Clark, date: 06/20/2013, view: 7239, Q&A: 0
    [Abstract] High throughput RNA Sequencing has revolutionized transcriptome analyses. However, most available protocols require micrograms of RNA rendering this technique not feasible for analyzing small numbers of cells, including precious rare cell types isolated from human tissues or organs. Here, we used an RNA Amplification System and describe a method ...
    Preparation of cDNA Library for dRNA-seq
    Authors:  Feng Li and Barbara Baker, date: 12/05/2012, view: 7973, Q&A: 0
    [Abstract] microRNAs (miRNAs) are ubiquitous regulators of gene expression in eukaryotic organisms, which guide Argonaute proteins (AGO) to cleave target mRNA or inhibit its translation based on sequence complementarity. In plants, miRNA directed cleavage occurs on the target mRNA at about 10 to 11 nucleotide (nt) up stream to the site where the 5’ end of ...
    Gene Networks Based on the Graphical Gaussian Model
    Author:  Shisong Ma, date: 02/20/2012, view: 8546, Q&A: 1
    [Abstract] This protocol describes how to build a gene network based on the graphical Gaussian model (GGM) from large scale microarray data. GGM uses partial correlation coefficient (pcor) to infer co-expression relationship between genes. Compared to the traditional Pearson’ correlation coefficient, partial correlation is a better measurement of direct ...