mul1_regions

A data.frame with GenIE regions details for the MUL1 example.

datasets

The R package for GenIE analysis is designed to analyze the next-generation sequencing
output from a set of GenIE experimental replicates. GenIE (genome-editing interrogation of enhancers)
is an experimental method to evaluate the effects of individual single-nucleotide polymorphisms (SNPs)
on gene transcription. It is based on targeted CRISPR-Cas9 genome editing in cultured cells to
produce indels at a target locus, optionally with a homology-dependent recombination (HDR) construct
to create precisely defined genomic changes. Following this, both genomic DNA (gDNA) and RNA are
extracted from the same pool of cells, then complementary DNA (cDNA) is generated from the RNA. Both
gDNA and cDNA are amplified with locus-specific PCR primers, in multiple replicates, and libraries of
the experimental replicates are prepared for next-generation sequencing. The sequencing data from each
replicate for each region should be aligned to either the full reference genome or to a locus-specific
(amplicon) reference genome for analysis by 'rgenie'.

Jeremy Schwartzentruber

rgenie

Analysis of GenIE Experiments

mul1_regions function

A data frame with 1 row and 9 variables:<dl class="dl-horizontal">
 <dt>name</dt><dd>region name</dd>
 <dt>sequence_name</dt><dd>chromosome or amplicon name</dd>
 <dt>start</dt><dd>start coordinate of the region</dd>
 <dt>end</dt><dd>end coordinate of the region</dd>
 <dt>highlight_site</dt><dd>coordinate of the SNP site</dd>
 <dt>cut_site</dt><dd>coordinate of the cut site</dd>
 <dt>hdr_allele_profile</dt><dd>HDR allele profile</dd>
 <dt>wt_allele_profile</dt><dd>WT allele profile</dd>
 <dt>ref_sequence</dt><dd>sequence of the amplicon region</dd>
</dl>

Format

GenIE regions for the MUL1 example. — mul1_regions

A data frame with 1 row and 9 variables:<dl class='dl-horizontal'>
 <dt>name</dt><dd>region name</dd>
 <dt>sequence_name</dt><dd>chromosome or amplicon name</dd>
 <dt>start</dt><dd>start coordinate of the region</dd>
 <dt>end</dt><dd>end coordinate of the region</dd>
 <dt>highlight_site</dt><dd>coordinate of the SNP site</dd>
 <dt>cut_site</dt><dd>coordinate of the cut site</dd>
 <dt>hdr_allele_profile</dt><dd>HDR allele profile</dd>
 <dt>wt_allele_profile</dt><dd>WT allele profile</dd>
 <dt>ref_sequence</dt><dd>sequence of the amplicon region</dd>
</dl>

mul1_regions: GenIE regions for the MUL1 example.

Description

Usage

Arguments

Format