Brunello_Library: Genome-wide annotation for the Brunello sgRNA library

In francescojm/CRISPRcleanR: Unsupervised correction of gene independent cell responses to CRISPR-cas9 targeting

Genome-wide annotation for the Brunello sgRNA library

Description

A data frame with a named row for each sgRNA of the Brunello sgRNA library [1] including annotations such as targeted genes, and genomic coordinates.

Usage

data(Brunello_Library)

Format

A a row named data frame with 76379 observations of the following variables (among others)

CODE

alphanumerical identifier of the sgRNAs;

GENES

targeted gene;

STARTpos

starting genomic coordinate of the targeted genomic region (numeric);

STRAND

targeted DNA strand ('sense' or 'antisense')

EXONE

exone of the targeted genomic region (exone number);

CHRM

chromosome of where the targeted region resides (string)

ENDpos

ending genomic coordinate of the targeted genomic region (numeric).

seq

nucelotidic sequence of the sgRNAs without the PAM. (string).

Source

Addgene website (catalog number: 73179; file: broadgpp-brunello-library-contents.txt, url: https://www.addgene.org/static/cms/filer_public/8b/4c/8b4c89d9-eac1-44b2-bb2f-8fea95672705/broadgpp-brunello-library-contents.txt)

References

[1] Doench JG, Fusi N, Sullender M, Hegde M, Vaimberg EW, Donovan KF, et al. Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9. Nat Biotechnol. 2016;34:184-91.

[2] Ong SH, Li Y, Koike-Yusa H, Yusa K. Optimised metrics for CRISPR-KO screens with second-generation gRNA libraries [published correction appears in Sci Rep. 2018 Apr 12;8(1):6136]. Sci Rep. 2017;7(1):7384. Published 2017 Aug 7. doi:10.1038/s41598-017-07827-z

Examples

## Not run: 
## Loading sgRNA Brunello library annotation file
data(Brunello_Library)
## Visualising first entries
head(Brunello_Library)

## Deriving the path of an example count file
## from screening the HT-29 cell line with the Brunello library
## [2]

fn<-paste(system.file('extdata', package = 'CRISPRcleanR'),
          '/HT29-Brunello_counts.tsv',sep='')

expName<-'HT29-Brunello'

## Loading, median-normalizing and computing fold-changes
normANDfcs<-
    ccr.NormfoldChanges(filename = fn,
                        display = TRUE,
                        min_reads = 30,
                        EXPname = expName,
                        libraryAnnotation = Brunello_Library)

## Genome-sorting the fold changes
gwSortedFCs<-
    ccr.logFCs2chromPos(foldchanges = normANDfcs$logFCs,
                        libraryAnnotation = Brunello_Library)

## Identifying and correcting biased sgRNAs' fold changes
correctedFCs_and_segments<-
    ccr.GWclean(gwSortedFCs = gwSortedFCs,
                display=TRUE,
                label=expName)

## End(Not run)

francescojm/CRISPRcleanR documentation built on April 30, 2023, 5:41 a.m.