Bioinformatics Workshop: PacBio Full-Length Single-Cell Kinnex

Basic Information:

Wednesday - Friday May 28-30, 2025, 9 a.m. - 4 p.m (Wed/Thurs, Remote) 10 a.m. - 2 p.m. (Friday, Remote/In-Person Mission Bay)

Organizer - UCSF CAT Bioinformatics

Contact - [email protected]

Location - Hybrid Wed/Thurs Remote and Friday both Remote and In Person Genentech Hall, Teaching Lab Room 227

Cost - UC and Affiliate Rate: $1200, Other Academic/Non-Profit: $1500, For-Profit: $2000 all per person

via CAT iLabs submission under 'CAT Bioinformatics: Workshop', the Credit Card option is not available this time.

Seats Available - 25 Seats

Workshop Description:

Unlocking Transcriptomic Complexity at Single-Cell Resolution with Kinnex and PacBio Long Reads

This workshop explores the power of combining Kinnex single-cell RNA-seq library preparation with PacBio Revio long-read sequencing. Discover how the Iso-Seq method enables in-depth, transcript-level profiling of individual cells, revealing differential transcript usage and providing insights into cellular heterogeneity and underlying pathology beyond gene-level analysis.

This is a Three-day hybrid remote/in-person workshop.

Day 1-2: Processing single-cell long-read data: command-line tools for demultiplexing, alignment, and generating cell-specific transcripts and counts. Day 2 includes isoform discovery and abundance estimation.

Day 3: Initial Single-cell analysis in command line and R: transcript and gene-level analysis, workflow creation/modification, and data quality assessment.

Sprinkled within will be additional talks and conversations, including experimental design, data generation, and philosophy of analysis.

Prerequisites:

This course does not provide instruction in the basics of the command line or R for bioinformatics. To get the most out of the workshop an intermediate understanding of the command line and the R statistical programming language are necessary.

All work will be performed on each individual's laptop using a small data set created specifically for the course and to complete in the time alloted.

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Cancellation Policy:

Registrants are requested to be cognizant that only so many seats for a workshop may be available and should notify the Core ([email protected]) as soon as they know they are unable to attend so that we can notify and accept someone on the waitlist that a spot has become available.

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Referencing the CAT Core and Publications

When submitting manuscripts, please acknowledge the CAT by including the text: “Sequencing was performed at the UCSF CAT, supported by UCSF PBBR, RRP IMIA, and NIH 1S10OD028511-01 grants.”

To aid our facility in future grant submissions, it helps to reference labs and publications that have benefited from our core please notify us of your achievement by emailing catcore [at] ucsf.edu the PMID number, lab, and the piece of equipment used in the paper.

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