Link to access protocols and reagents in Synapse:

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 28^th through the 30^th at Stanford University, in conjunction with the 6^th 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:

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.