Randomized Sequence Pool
Randomized Sequence Pool - Related Videos
14:06
Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER
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Cited by 10 •
2012
Pooled DNA sequencing is a fast and cost-effective strategy to detect rare variants associated with complex phenotypes in large cohorts. Here we describe the computational analysis of pooled, next-generation sequencing of 32 cancer-related genes using the SPLINTER software package. This method is scalable, and applicable to any phenotype of interest.
00:09
Pooled CRISPR-Based Genetic Screens in Mammalian Cells
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Cited by 13 •
2019
CRISPR-Cas9 technology provides an efficient method to precisely edit the mammalian genome in any cell type and represents a novel means to perform genome-wide genetic screens. A detailed protocol discussing the steps required for the successful performance of pooled genome-wide CRISPR-Cas9 screens is provided here.
11:14
Primer-Free Aptamer Selection Using A Random DNA Library
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Cited by 23 •
2010
SELEX protocols comprise multiple rounds of selection, each of which require regeneration of bound ligands, which in turn require fixed primer sequences flanking the random library regions. These fixed primer sequences can interfere with the selection process (false positives and negatives). Here we present a primer-free protocol.
09:12
MISSION LentiPlex Pooled shRNA Library Screening in Mammalian Cells
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Cited by 10 •
2011
Here we use a human LentiPlex pooled library and traditional sequencing methods to identify gene targets promoting cell survival. We demonstrate how to set up and deconvolute a LentiPlex screen and validate the results.
08:57
Amplicon Sequencing using the Long-Read Sequencing Technologies
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2025
This protocol was optimized for targeted deep sequencing of 18 drug-resistance regions in Mycobacterium tuberculosis using a long-read sequencing platform, followed by analysis with a tuberculosis-specific bioinformatics pipeline designed for long-read data.
FAQs
Defined random or degenerate positions introduce alternative nucleotides at selected locations during oligonucleotide synthesis. This creates many related DNA or RNA molecules that differ in sequence composition while retaining the designed regions around those positions. Researchers can therefore examine how sequence changes affect binding, regulation, or activity within a single parallel experimental framework.
Selection applies chosen conditions that favor molecules with a desired property, such as binding or altered activity. Sequencing the pool before and after selection allows researchers to compare sequence representation and identify molecules that become enriched. Enrichment provides a link between particular sequence compositions and the biological function being tested.
A pool presents many sequence variants to the same experimental system, allowing their behavior to be evaluated under shared conditions. This parallel design supports comparisons among variants rather than testing each sequence separately. The resulting sequence-function relationships can reveal regulatory elements, binding motifs, or variants associated with changed activity.
The selected conditions determine which molecules are retained, detected, or enriched during screening. Consequently, a sequence may emerge as a candidate because it performs well under the particular conditions used, rather than under every possible condition. Comparing enrichment under defined conditions helps connect sequence composition with the function being investigated.
Researchers first synthesize oligonucleotides containing defined random or degenerate positions, then amplify or express the resulting molecules when required by the experiment. The pool is screened under selected conditions, followed by sequencing before and after selection. Comparing these sequence datasets identifies enriched candidates for further genetic or functional analysis.
These pools can support discovery of regulatory elements and binding motifs, as well as variants with altered activity. They also provide a way to investigate aptamers, which are nucleic acid candidates identified through sequence-based selection. In genetics research, the resulting candidates can guide further experimental design and focused testing of sequence-function relationships.