Workshop on Single Cell ATAC-seq for Chromatin Accessibility Profiling
Learn how to use ATAC-seq (Assay for Transposase-Accessible Chromatin using high throughput sequencing) to identify chromatin accessibility of single cells at Penn Program in Single Cell Biology.
Techniques include
- Single cell isolation - patch pipette, Isoraft
- Tagment genomic DNA - Nextera Transposomes
- Amplify tagmented DNA - Nextera DNA Flex Library Kit
- Sequencing data analysis using VisCello
Dates: Monday, October 28 – Tuesday, October 29, 2019
Schedule: 9am - 5pm daily
Location: Room 24, John Morgan Building
Cost: $150
Open to: Penn faculty, postdocs and graduate students
Application deadline: Friday, October 18, 2019
Places are limited. To apply, complete the application form (available here) and email it, along with a two-page CV, to Jifen Li. Successful applicants will be notified on Monday, October 21.
Contact: Jifen Li, PhD, Associate Director of Programs, PPSCB
jifenli@pennmedicine.upenn.edu
Sponsors: ITMAT and Penn Program in Single Cell Biology
Workshop on Single Cell Transcriptomics for Cellular Phenotyping
The PENN Program in Single Cell Biology (PPSCB) is offering a workshop on single cell transcriptome analysis using linear aRNA amplification and SMART-seq.
Techniques include
- Single cell isolation - patch pipette, Isoraft
- RNA amplification - linear amplification (aRNA), SMART-seq2
- Preparation of single cell libraries for Illumina sequencing
- RNA-seq data analysis using VisCello
Dates: Monday, October 14 – Friday, October 18, 2019
Schedule: 9am - 5pm daily
Location: Room 24, John Morgan Building
Cost: $500
Open to: Penn faculty, postdocs and graduate students
Application deadline: Friday, October 4, 2019
Places are limited. To apply, complete the application form (available here) and email it, along with a two-page CV, to Jifen Li. Successful applicants will be notified on Monday, October 7.
Contact: Jifen Li, PhD, Associate Director of Programs, PPSCB
jifenli@pennmedicine.upenn.edu
Sponsors: ITMAT and Penn Program in Single Cell Biology
Previous Workshops
Smart-Seq and Library Preparation Workshop
Rapidly amplify single cell RNA using SMART-seq2 technology and prepare libraries for RNA-seq. Learn about the mechanisms behind the techniques and the advantages of working with single cells.
Techniques include
- Single cell isolation - patch pipette, Isoraft
- RNA amplification - SMART-seq2
- Library preparation – Illumina Nextera DNA Library Preparation Kit
- RNA-seq data analysis using PIVOT
Dates: Tuesday, August 15 – Wednesday, August 16, 2017
Location: The University of Pennsylvania Perelman School of Medicine
Sponsors: ITMAT and Penn Program in Single Cell Biology
Workshop on Single Cell Transcriptomics for Cellular Phenotyping
Could single cell transcriptomics advance your research?Learn high throughput single-cell RNA sequencing technologies from leaders in the field at the University of Pennsylvania’s Penn Program in Single Cell Biology.
Techniques include:
- Single cell isolation - patch pipette, Isoraft, Fluidigm C1
- RNA amplification - linear amplification (aRNA), Smart-seq
- Image-based methods (TIVA, TISA)
- RNA-seq library preparation (Illumina TruSeq Stranded and Nextera Kit)
- RNA-Seq data analysis (KimLabIDV)
Dates: Monday, March 13 – Friday, March 17, 2017
Location: The University of Pennsylvania Perelman School of Medicine
Course Instructors: Drs. James Eberwine, Junhyong Kim, Jifen Li and others.
Sponsors: NHGRI, ITMAT, Penn Program in Single Cell Biology, Illumina and Clontech Laboratories.
Single Cell Transcriptomics Workshop
The PENN Program in Single Cell Biology is offering a workshop on single cell transcriptome analysis using linear aRNA amplification and SMART-seq.
Techniques include
- Single cell isolation - patch pipette, Isoraft
- RNA amplification - linear amplification (aRNA), Smart-seq2
- Preparation of single cell libraries for Illumina sequencing
- RNA-Seq data analysis using KimLabIDV
Dates: Monday, January 23 – Friday, January 27, 2017
Location: The University of Pennsylvania Perelman School of Medicine
Open to: Penn faculty, postdocs and graduate students
Sponsors: ITMAT, Penn Program in Single Cell Biology, Illumina and Clontech Laboratories.
Smart-Seq and Library Preparation Workshop
Learn to use the SMART-seq2 protocol to generate sequencing libraries from single cells.
Techniques include
- Single cell isolation - patch pipette, Isoraft
- RNA amplification - Smart-seq2
- Library preparation – Illumina Nextera DNA Library Preparation Kit
- Single-cell gene expression analysis using KimLabIDV
Dates: Tuesday, August 16 – Wednesday, August 17, 2016
Location: The University of Pennsylvania Perelman School of Medicine
Open to: Penn faculty, postdocs and graduate students
From Single Cell to RNA-Seq
Could single cell expression profiling advance your research?
The PENN Program in Single Cell Biology is offering a workshop on linear amplification of RNA (aRNA) from single cells and sample preparation for RNA-Seq.
- Learn on primary neurons
- Bring your own samples (in consultation with Dr. Li)
- Harvest single cells using a patch pipette
- Produce aRNA from each cell using linear amplification
- Prepare single cell libraries for Illumina sequencing
- Learn how the techniques work and how single cell biology can augment your research
- Generate preliminary data for your grant proposal
Dates: Monday, May 9 – Friday, May 13, 2016
Location: The University of Pennsylvania Perelman School of Medicine
Open to: Penn faculty, postdocs and graduate students.
National Single Cell Transcriptomics Workshop
Learn advanced techniques for single cell isolation, RNA amplification and gene expression profiling by RNA-seq from leaders in the field at the University of Pennsylvania’s Penn Program in Single Cell Biology.
The data that participants collected during the workshop is available for public download here.
Techniques include:
- Single cell isolation - patch pipette, Isoraft, Fluidigm C1
- RNA amplification - linear amplification (aRNA), Smart-seq
- Image-based methods
- RNA-seq library preparation
- Basic informatics
Participants may bring their own samples, on consultation with course instructors.
Dates: Mon, 4th May – Fri, 8th May 2015
Location: The University of Pennsylvania Perelman School of Medicine
Course Instructors: Dr. James Eberwine, Dr. Junhyong Kim, Dr. Catherine Moorwood and others.
Sponsors: NHGRI, ITMAT, Penn Program in Single Cell Biology, Illumina, Clontech Laboratories and Fluidigm.
Smart-Seq and Libraries Workshop
Rapidly amplify single cell RNA using Smart-seq technology and prepare libraries for RNA-seq. Learn about the mechanisms behind the techniques and the advantages of working with single cells. Participants may bring their own samples (on consultation with Dr. Moorwood). If you wish to do this, and have not isolated single cells before, the Single Cell Isolation Workshop (see above) is recommended!
Dates: Thu, 19th Mar - Fri, 20th Mar, 2015Location: Room 24, John Morgan Building
Instructors: Dr. James Eberwine, Dr. Junhyong Kim, Dr. Catherine Moorwood
Single Cell Isolation Workshop
Bring your own samples (on consulation with Dr. Moorwood) and learn how to isolate single cells using a patch pipette or Cell Microsystems Isoraft technology.
Date: Fri, 13th Mar, 2015Location: The University of Pennsylvania Perelman School of Medicine
Instructor: Dr. Catherine Moorwood
Open to: Penn faculty, trainees, senior research investigators and graduate students
Linear RNA Amplification (aRNA) Workshop
The PENN Program in Single Cell Biology is offering a workshop on linear amplification of RNA (aRNA) from single cells and sample preparation for RNA-Seq.
- Bring your own samples (upon consultation with Dr. Moorwood)
- Harvest single cells using a patch pipette or Cell Microsystems Isoraft technology
- Produce aRNA from each cell using linear amplification
- Prepare single cell libraries for Illumina sequencing
- Learn how the techniques work and how single cell biology can augment your research
- Generate preliminary data for your grant proposal
Dates: Monday, 1st Dec – Friday, 5th Dec 2014
Location: The University of Pennsylvania Perelman School of Medicine
Open to: Penn faculty, postdocs and graduate students
