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Introduction to Single-cell RNA-seq analysis Harvard Chan Bioinformatics Core https://tinyurl.com/hbc-intro-to-scrnaseq

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Introduction to Single-cell RNA-seq analysis

Harvard Chan Bioinformatics Core

https://tinyurl.com/hbc-intro-to-scrnaseq

Page 2: Introduction to Single-cell RNA-seq analysis · Describe steps in a Single-cell RNA-seq analysis workflow. Use Seurat and associated tools to perform analysis of single-cell expression

Rory KirchnerJohn HutchinsonAssociate Director Victor BarreraShannan Ho Sui

Director Zhu Zhuo

James Billingsley Peter KraftFaculty AdvisorSergey NaumenkoIlya Sytchev Joon Yoon

Radhika KhetaniTraining DirectorMary PiperMeeta Mistry Jihe LiuPreetida Bhetariya

Page 3: Introduction to Single-cell RNA-seq analysis · Describe steps in a Single-cell RNA-seq analysis workflow. Use Seurat and associated tools to perform analysis of single-cell expression

Rory KirchnerJohn HutchinsonAssociate Director Victor BarreraShannan Ho Sui

Director Zhu Zhuo

James Billingsley Peter KraftFaculty AdvisorSergey NaumenkoIlya Sytchev Joon Yoon

Radhika KhetaniTraining DirectorMary PiperMeeta Mistry Jihe LiuPreetida Bhetariya

Page 4: Introduction to Single-cell RNA-seq analysis · Describe steps in a Single-cell RNA-seq analysis workflow. Use Seurat and associated tools to perform analysis of single-cell expression

Consulting

• RNA-seq, small RNA-seq and ChIP-seq analysis

• Genome-wide methylation

• WGS, resequencing, exome-seq and CNV studies

• Quality assurance and analysis of gene expression arrays

• Functional enrichment analysis

• Grant support

Page 5: Introduction to Single-cell RNA-seq analysis · Describe steps in a Single-cell RNA-seq analysis workflow. Use Seurat and associated tools to perform analysis of single-cell expression

NIEHS / CFAR Bioinformatics

Core

Center for Stem Cell

Bioinformatics

Harvard Catalyst

Bioinformatics Consulting

HMS Tools &

Technology

Page 6: Introduction to Single-cell RNA-seq analysis · Describe steps in a Single-cell RNA-seq analysis workflow. Use Seurat and associated tools to perform analysis of single-cell expression

Training

We have divided our short workshops into 2 categories:

1. Basic Data Skills - No prior programming knowledge needed (no prerequisites)

2. Advanced Topics: Analysis of high-throughput sequencing (NGS) data - Certain “Basic” workshops required as prerequisites.

Any participants wanting to take an advanced workshop will have to have taken the appropriate basic workshop(s) within the past 6 months.

http://bioinformatics.sph.harvard.edu/training/ https://hbctraining.github.io/main/

https://hbctraining.github.io/main/training_spring2019.html#basic-data-skills

https://hbctraining.github.io/main/training_spring2019.html#advanced-topics-analysis-of-high-throughput-sequencing-ngs-data

https://hbctraining.github.io/main/training_spring2019.html#basic-data-skills

http://bioinformatics.sph.harvard.edu/training/

https://hbctraining.github.io/main/

Page 7: Introduction to Single-cell RNA-seq analysis · Describe steps in a Single-cell RNA-seq analysis workflow. Use Seurat and associated tools to perform analysis of single-cell expression

Workshop scope

Page 8: Introduction to Single-cell RNA-seq analysis · Describe steps in a Single-cell RNA-seq analysis workflow. Use Seurat and associated tools to perform analysis of single-cell expression

Bioinformatics data analysis

http://anoved.net/tag/lego/page/3/

Page 9: Introduction to Single-cell RNA-seq analysis · Describe steps in a Single-cell RNA-seq analysis workflow. Use Seurat and associated tools to perform analysis of single-cell expression

Learning objectives

Learning Objectives

✓ Describe best practices for designing a Single-cell RNA-seq experiment

✓ Describe steps in a Single-cell RNA-seq analysis workflow.

✓ Use Seurat and associated tools to perform analysis of single-cell expression data, including data filtering, QC, integration, clustering, and marker identification

Logistics

Page 11: Introduction to Single-cell RNA-seq analysis · Describe steps in a Single-cell RNA-seq analysis workflow. Use Seurat and associated tools to perform analysis of single-cell expression

�11

https://tinyurl.com/hbc-intro-to-scrnaseq

Page 12: Introduction to Single-cell RNA-seq analysis · Describe steps in a Single-cell RNA-seq analysis workflow. Use Seurat and associated tools to perform analysis of single-cell expression

Odds and Ends

✤ Name tags: Tent Cards ✤ Post-its ✤ Phones on vibrate/silent!

Page 13: Introduction to Single-cell RNA-seq analysis · Describe steps in a Single-cell RNA-seq analysis workflow. Use Seurat and associated tools to perform analysis of single-cell expression

Training team : [email protected]

Consulting : [email protected]

@bioinfocore

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