GMUSCLE

Genotyping MUltiplexed-Sequencing of CRISPR-Localized Editing

CRISPR-Cas9 gene editing is widely used to create genetic modified cells. The genetic editing results in cellular heterogeneity, allelic diversity, and randomness of de-novo sequences, which constitute a major challenge in genotyping CRISPR-Cas9-edited cells.

We introduce a streamlined and cost-effective protocol along with the computational tool GMUSCLE, to sequence and genotype the products of CRISPR-Cas9 gene editing with great depth, high accuracy, high efficiency, and handy utilization.

GMUSCLE enables the quantitative and qualitative identification of the genotypes of CRISPR-Cas9-edited cells from sequencing data.

Reference: Zhang P., et al. Genotyping MUltiplexed-Sequencing of CRISPR-Localized Editing (GMUSCLE): An experimental and computational approach for analyzing CRISPR-edited cells. The CRISPR Journal. 2023. [PMID:37824834] [Paper]

Human Reference Genome:
GRCh37
GRCh38

Chromosome: [chr1-22, chrX, chrY]
Start Position: [integer, > 0]
End Position: [integer, > 0]
Read Count Cutoff: [integer, >= 0]
Genotype Proportion Cutoff: [decimal, 0 ~ 1]
Upload Data:

Single Sample
Provide the demultiplexed fastq.gz of one sample. [example]
The targeted genomic region of the example is: chr21-34715869-34716164 (GRCh37).

Read Type:
Single-end

Pair-end
R1:
R2:

Multiple Samples
Provide the demultiplexed fastq.gz of multiple samples, in one compressed .zip file. [example]
Provide the sample names (one sample per line, without '.fastq.gz') in a text file. [example]
The targeted genomic region of the example is: chr21-34715869-34716164 (GRCh37).
If data is pair-end, their fastq should be named as '_R1.fastq.gz' and '_R2.fastq.gz'.

Read Type: Single-end Pair-end
Sample FASTQ:
Sample Names:

Note:
Please use fastq.gz for using the webserver, for a faster data receiving and processing.
Please limit your upload less than 100 MB. For larger data, please visit standalone version.
Genotypes < 1% won't be plotted, but will be available in the output summary and tables.
Indels that are beyond the given genomic region won't appear in the alignment file.

GMUSCLE

GMUSCLE

Genotyping MUltiplexed-Sequencing of CRISPR-Localized Editing

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Developer| Peng ZHANG Ph.D.

Lab Head| Jean-Laurent CASANOVA M.D., Ph.D.

Laboratory| St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University

Last Update| Oct 17, 2023

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