Cheap Targeted Deep Sequencing For CRISPR Experiments

May 10, 2018

BlueskyReddit
Neurobiology
Harvard Medical School
Postdoctoral Fellow

Overall

Quality of Results

Ease-of-Optimization

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Company:

MGH CCIB DNA Core

Service Provided:

CRISPR sequencing

This service is extremely useful for someone who is interested in quantifying CRISPR action on target genes. PCR amplicons could be sent to the facility, where library construction and deep sequencing is performed for only ~$70 (academia, non-profit). Usually, 100K reads are generated. Analysis service is also available. It's highly recommended and cost effective for researches who don't have expertise/time to build DNA libraries and perform their own MiSeq sequencing.

Experimental Design and Results Summary

Downstream Applications

FASTQ files are generated.

Timeline

10 days

Nature of Service

Sequencing

Technical Service

Extremely good. They can handle difficult requests and can even accommodate the pipeline to individual needs.

Delivery

Very few issues. Rarely, read numbers are low, but in this case they repeat the sequencing for free (sample amount sufficient for two runs).

Results Summary

Sample submission requirements are found on the website:https://dnacore.mgh.harvard.edu/new-cgi-bin/site/pages/crispr_sequencing_pages/crispr_sequencing_submission.jspThis includes design of the PCR amplicon, submission requirements. Samples can be shipped to the facility (https://dnacore.mgh.harvard.edu/new-cgi-bin/site/pages/sequencing_pages/seq_submission.jsp) or can be picked in the Boston area.Important parameters: 2x150bp paired end sequencing is performed on the MiSeq machine, 100K reads are generated/sample. aResults are delivered within 10 days.

DOI or PMID #

N/A

Image Gallery

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Summary

The Good

Easy, cost-efficient, very informative.

The Bad

If you have multiple samples, it gets expensive (consider running on your own).

The Bottom Line

I have sequenced hundreds of PCR amplicons with this service. If you are not very experienced with CRISPR readouts or don't have too many samples, this option is great for you. FASTQ files are usually very high quality and adapters are already removed. They provide some analysis, but I don't have experience with that. Link to site: https://dnacore.mgh.harvard.edu/new-cgi-bin/site/pages/crispr_sequencing_main.jsp

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