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BCBC Website Version 4.6 Released

Jan 17, 2012 - Nashville, TN

We are pleased to announce the release of version 4.6 of the Betacell.org website. As always, we welcome your feedback.

New & Improved Features

New Resources

New Research Highlight

The Human ESC Differentiation Protocols research highlight exhibits a collection of protocols representing the efforts of four BCBC investigators, Gordon Keller, Henrik Semb, Doug Melton, and Maike Sander, to take human embryonic stem cells and differentiate them into pancreatic endocrine cells.

Tools to Help Members with BCBC Policies & Guidelines Compliance

When BCBC 3.0 Investigators, Co-investigators, or Affiliates log on to Betacell.org, the web application checks if there are any issues keeping that BCBC member from being in full compliance with the BCBC Policies & Guidelines.  If there are any such issues, you will be redirected to a Member Compliance page that explains the issues and what you can do to remedy them. There will also be a banner at the top of your Dashboard leading to the Member Compliance page.

New Core Facility Workspaces

There are three new workspaces to support these new BCBC Core Facilities, in addition to Core Services pages for each (manageable by Core Directors):

Training Travel Awards Application Page

If BCBC 3.0 Affiliates travel to other BCBC laboratories to  receive (or provide) short-term, focused training in scientific techniques or technologies, they can apply to be reimbursed for travel expenses on the new Training Travel Award Program page.

Improvements to the Resource Request System

A number of small improvements were made to the Resource Request System.  One large improvement: workspace member may set Inventory items corresponding to the data resources (Protocols, Studies, and Miscellaneous Resources) as “Auto Fill”.  If this option is selected, then any requests by BCBC members for that Resource will be automatically filled.  The intent of this feature is to let you grant access to data resources without the level of fuss necessitated by requests for tangible reagents.

Improvements to Workspace Document Uploads

Some workspaces were rapidly amassing a lot of uploaded documents, so we added the ability to define virtual folders.

Improvements to Betacell.org Site Search

We replaced our old method of searching the website with a custom Google search engine.

Search Page Updated - Beta Cell Genomics

The former Queries page has been redesigned and renamed as the Search page with Studies, Genes, Genomic Locations (new!), Relationships, and Transcripts. Click on them to open or close.

  • Studies. The Expression data section has been replaced with Analysis offering searches for Available Gene Lists, Available Location Lists, Gene Differential Expression, and Peaks.
  • Genes. We've added a Gene Type query under Annotation. This will be useful especially in combination with searches for peaks or DNA motifs and you'd like to see if there are, for example, any protein-coding genes nearby. The Homologous Genes search has been moved to the Names or Identifier section. A new subsection, Genomic Location, has been added with a Location search to find genes in a specified genomic region. The Diabetes Candidate Region search has also been moved there.
  • The new Genomic Location section has searches for Location or Identifier where you can also upload your own list. Under Similarity or Pattern there is a search for DNA motifs that can used to search for transcription factor binding sites or other genomic signals.
  • The Relationships section remains the same.

Ability to search for genomic regions of interest added - Beta Cell Genomics

New Genomic Location searches have been added that enable you to:

  • Access specified regions of interest. For these you can get the sequence, see what genes are located, and get a list of peak calls from Beta Cell Genomics studies in that region.
  • Get a list of genomic regions from selected study summary pages. These might be ChIP-seq or microarray-based peak calls. You can also upload a file of regions from your own study.
  • Search for DNA motifs. For example, you can look for TFBS by specifying a consensus motif.

Ability to combine searches for genes and genomic regions - Beta Cell Genomics Search Page Updates

The Strategies search mechanism has been augmented with co-location operations that allow you to look for overlap between genes and genomic regions of interest (e.g., peak calls). An example strategy will be made available on the My Strategies page in the Examples tab.

New Resources

Antibodies (8)

Genomics Studies

Three new studies have been added. The Study Summary page has been updated to directly provide information on study design, study factors, and the assays. Use the graph link to see the study work flow; click on the boxes to get details about samples, protocols, and data.

  1. Whole transcriptome analysis of Sox17.Epi and Endo cells in mouse embryos (Magnuson lab)
    Gene expression profiles in Sox17.Epi and Endo cells were generated using multiplex RNA-Seq technology. Sox17.Epi (Sox17^GFP+EpCAM+) and Sox17.Endo (Sox17^GFP+EpCAM-) cells were isolated by FACS from E9.5 mouse embryos. Details are available here.
    We have added a track to the genome browser showing results from this study.
    BCBC access.
  2. Transcriptional profiling of Insm1-dependent pancreatic endocrine differentiation (Magnuson lab)
    RNA-Seq technology was used to explore gene expression in mouse Insm1^GFP/+ [het] FACS sorted pancreatic cells at E15.5 (commited endocrine progenitor cells) and in Insm1^GFP/GFP [null] at E15.5 (defective endocrine progenitor cells). Details are available here.
    BCBC access.
  3. Transcriptional and epigenetic profiling of the progression of hESCs to beta cells
    Genome-scale maps of H3K4me3, H3K4me1 and H3K27me3 patterns by ChIP-seq and expression profiles by RNA-seq from undifferentiated human ESCs, three intermediate differentiated stages (definitive endoderm, primitive gut tube, and posterior foregut), pancreatic progenitors and in vitro-differentiated polyhormonal cells have been generated. Details are available here.
    BCBC access.

Misc. Resources (1)

Mouse ESC Lines (7)

Mouse Strains (6)

Protocols (14)