Synapse

The PCBC Bioinformatics Core has put together all of the available genomic scale data from the Cincinnati Cell Characterization Core (C4) in one location, Synapse.  This initial dataset consists of 181 mRNA samples, 123 miRNA samples, and 33 methylation samples from 10 different labs. In addition to the summarized data, the PCBC Bioinformatics Core is also providing the raw sequencing data, information about the sequencing pipeline, and comprehensive comparative analysis across expression and alternative splicing.  The goal is for this resource to grow both with other analysis and data.

Instructions for generating a Synapse account:

1) Register for a Synapse account:
2) Request access to the PCBC project by visiting: https://www.synapse.org/#!Team:2224090 and click Request to Join Team.  Please include your association  with the PCBC in the message.
 
3) Once you have been given access, the project content is available at:
 
If you need any assistance with Synapse, please contact Larsson Omberg at (larsson.omberg@sagebase.org ).
 

Link to access protocols and reagents in Synapse:


 

Past Hands-on Training at Stanford University:

The PCBC Bioinformatics Hub has assembled, analyzed, and made available for further focused analyses, a series of genomic profiling data that encompasses gene, transcript, and miR expression as well as genomic DNA methylation of a large bank of human embryonic stem cells, induced pluripotent stem cells, and mesoderm, endoderm, and ectoderm lineage differentiated cells from many different cell lines.

With the massive amount of genomics data available, both within PCBC research hubs and the public domain, it is essential that researchers have the appropriate tools to analyze this data. The PCBC Bioinformatics Core was created to ensure that researchers within the PCBC have streamlined access to the significant data generated by the PCBC cell characterization core, easy-to-use tools to analyze and visualize this data, and the ability to apply these tools and data to specific research questions.

From Sunday, September 28th through the 30th at Stanford University, in conjunction with the 6th Annual PCBC Meeting, the Bioinformatics core hosted a series of tables to encourage any researchers to meet with members of the PCBC Bioinformatics Core. At these booths, the following works were done:

  1. Analysis of single-cell and bulk RNA-Seq data
  2. Navigation and download of the Synapse C4 data
  3. Integration of your data with C4 sequencing and array data
  4. Creation and visualization of WikiPathways
  5. Analysis and visualization of gene and splicing data in AltAnalyze
  6. Identification of key signatures from your data in ToppGene
  7. Creation of gene networks in Cytoscape
  8. Study design and other questions

 

The booths were made available by appointment and drop.  In addition to these, a WikiPathways curation event in conjunction with the Fellows Only Meeting (FOS) was held on Sunday, September 28, 2014. This event was aimed to create digital pathway references for progenitor differentiation to distinct cell lineages (heart, lung and blood related) to allow for the intelligent analysis of genomics data, to be published as a unique resource following the meeting.  For this event, investigators came with review articles or pathway figures in hand and be ready to work with others in designating key molecules and cell differentiation intermediate states.  If you were not present on these hands-on trainings and would like to get more information on specific questions, please contact us at: pcbc_bioinformatics@googlegroups.com

Note:

WikiPathways

The PCBC Bioinformatics Core will be posting a series of tutorials that will walk researchers through the process of creating reference digital pathways for analysis with their own omics data and those produced by the Cincinnati Cell Characterization Core (C4). It is recommended that people view these tutorials and follow along prior to group pathway creation or editing sessions. Check out the exciting flyers about what WikiPathways can offer to you via the link below:

/content/bioinformatics-and-genomics-tools


Recorded Webinars:

The PCBC Bioinformatics Core presented their second webinar:” Normalization, artifact detection and correction in Synapse” on Friday, August 29, 2014, at 12:00 Noon, PDT (1:00pm, MDT, 2:00pm, CDT, 3:00pm, EDT).

The second webinar covered the following topics:

* Principal component analysis and visualization

* Correlation analysis with covariates

* Corrections using Linear models

* Given enough time we will cover Surrogate Variable Analysis

 

Click on the link below to play this webinar recording:

http://youtu.be/ZcnSencVkEY

 

Title: Bioinformatics Core - Synapse Webinar

Date/Time: Thursday, December 19, 2013, 1:00 pm – 2:00 pm (EST)

Presenters: Bruce Arnonow, Larsson Omberg, Nathan Salomonis

Click on the link below to play this webinar recording:

https://epiumd.webex.com/epiumd/lsr.php?RCID=3c06c71fae59d471433f7540bbeece4a

 

Title/Date: Accessing PCBC Generated Data in Synapse, June 5, 2014

Presenter: Larsson Omberg

The following topics were covered:

  • how to access, download, and query PCBC generated data as stored in Synapse,
  • how to use the PCBC web portal in Synapse to perform hierarchal clustering of user specified genes and link out to enrichment analysis,
  • how to get started in accessing the data from within R and Python, and
  • how to store your own analysis results in Synapse.

As the series progresses, more advanced topics in genomics and bioinformatics from visualization to batch correction to differential expression analysis will be covered.

Click on the link below to view the recording of this webinar:

https://www.youtube.com/playlist?list=PL0QrRbpf8KbSO8eTNFsIPUZJ85u6gtNkQ

 

These bioinformatics webinars and tutorial videos are accessible from the PCBC Synapse resource platform, also.

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