News & Events
BCBC Website Version 4.7 Released
Apr 24, 2012 - Nashville, TN
We are pleased to announce the release of version 4.7 of the Betacell.org website. As always, we welcome your feedback.
New & Improved Features
The BCBC Bioimage Collection is a resource for the aggregation and dissemination of bioimages relevant to beta cell biology. It provides various tools to faciliate the visualization of imaging data. For example, it uses the Google Maps API to allow rapid zooming, panning, and annotation of large, high-resolution microscope images Also, Z-stacks can be easily visualized and interacted with.
The HIDEF CBP is imaging human fetal pancreas tissues aged 5-22 weeks to better understand endocrine cell specification, differentiation into hormone expressing lineages, islet organization and formation, and glucose-responsive insulin secretion. The HIDEF project has produced images using virtual slice technology and deep optical sectioning of wholemounts. The data represents approximately 500 z-stacks and images from 25-30 human fetal pancreas samples.
The Resource Request System (RRS) has been rebuilt to make the process of dealing with resource requests as simple and clear as possible for both requesters and suppliers. The RRS is tied into the dashboard so that requests needing your attention are highlighted. At each stage of the request process the RRS makes it clear whose turn it is to take action, and what actions are available. Also, if an affiliate requests a resource the name of their Principal Investigator is included in the request notification, and the Principal Investigator is CC’d on all RRS notifications concerning the request. Complex and potentially confusing features allowing suppliers to maintain multiple inventory items per resource did not appear to be useful and so have been removed.
- The Genome Browser has been upgraded to use GBrowse2 (version 2.39), with a more user-friendly interface. New features include:
- Genome browser tracks have been separated according to species.
- The user can upload his/her Custom Tracks.
- Ability to view BCBC restricted tracks upon logging in, in addition to the public study tracks.
- We have added a basket tool for genes. This allows a user to cherry pick individual genes and place them in the basket for further analysis.
- Steps in the Strategies can be used to transform lists of one type (e.g., Relationships of genes) to lists of another type (e.g., Genes). The following transformations have been added to the Strategies:
- Relationship Results to Gene Lists.
- Heatmap Lists to Gene Lists.
- Gene Lists to Heatmap Lists.
- Comparisons to Studies.
- HTS Analyses to Studies.
- Look and feel of the meta-analysis heatmaps and comparison profiles have been improved
- Reprogramming of mouse gall bladder cells into pancreatic beta cells BCBC access
This study used RNA-seq profiling to study transdifferentiation of gall bladder cells to beta cells. Mouse gall bladder cells from MIP-GFP mice were expanded in vitro and transduced with adenoviral vectors expressing the transcription factors Neurog3, Pdx1 and MafA. Reprogrammed GFP+ cells were then FACS-sorted for RNA isolation. (Grompe Lab)
- Epigenetics of human pancreatic cells BCBC access
RNA-seq and ChIP-Seq profiling (H3K4me3 and H3K27me3) of sorted human pancreatic alpha, beta, and exocrine cells was performed. (Kaestner Lab)
- Transcriptional profiling of Ngn3-dependent pancreatic endocrine differentiation at E15.5 BCBC access
This study used RNA-Seq profiling to explore gene expression in mouse Ngn3^GFP/+ [het] FACS sorted pancreatic cells at E15.5 (committed endocrine progenitor cells) and in Ngn3^GFP/GFP [null] at E15.5 (defective endocrine progenitor cells). This study is designed to understand the gene expression alteration in the endocrine lieage at different embryonic days. The aim is to understand both Ngn3 dependent and independent gene expression profiles so as to reveal the instructive signals that specify the collective endocrine islet cell fate or specific islet cell type. (Gu Lab)
- ChIP-Seq dataset for Ptf1a ChIP of chromatin from dissected, whole E17.5 mouse pancreas BCBC access
ChIP-Seq analysis of chromatin from whole E17.5 mouse pancreas was used to identify the genome-wide sites of bound Ptf1a, RbpjL and RbpJ. Tracks for this study are also visible on our Genome Browser upon logging in. (MacDonald Lab)
- Transcriptional profiling of nascent and mature pancreatic beta cells BCBC access
This study used RNA-Seq profiling to examine transcription profiles in FACS-sorted MIP-EGFP+ mouse pancreatic cells at E16.5 (nascent beta cells) and P60 (mature beta cells). Such an analysis should reveal the gene transcription alterations for beta cell development and for function. (Gu Lab)
- Frozen Section Staining_Tyramide Signal Amplification BCBC access
- Frozen Section Staining_Avadin/Biotin Amplification BCBC access
- Islet Transplantation Procedure BCBC access
- Preparing Islets for Transplant and Calculating IEQs BCBC access
- Tissue Culture Protocol for Expansion of Murine Gallbladder Cells BCBC access
- Isolation of Single Human Beta Cells – Identifying Somatic Mutations BCBC access
- Tissue culture protocol for expansion of human gallbladder cells BCBC access
- Differention of hESCs towards pancreatic like glucose-responsive insulin-secreting cells, in vitro BCBC access
- Human and Rodent Ocular Transplantation BCBC access