Why is there a new site?

In early 2010 we updated the site to facilitate more rapid transfer of our data to the public database and focus our efforts on the core mission of providing expression pattern images to the research community. The original database reproduced functions available on FlyBase, complicating our updates by the requirement to re-synchronize with FlyBase updates. Our expression reports on the new site still link to FlyBase gene reports, but we no longer reproduce FlyBase functions and therefore can update expression data on an ongoing basis instead of more infrequent major releases. All the functions relating to the expression patterns remain and we soon will add an option to search expression patterns by image similarity, in addition to annotation term searches. In a transitional phase we will leave both the old and the new sites up, but the newer data (post Release 2) will appear only on the new website. We welcome any feedback or requests for additional features.

How often are new data released?

Our first release was in 2002 with 2000 genes. The second release was in 2007 with 6000 genes. Release 3 in 2010 brings the total to 7000 genes including 97% of the sequence specific transcription factor genes. The 2010 update of the public database allows us to more make frequent, incremental additions to the database which will keep our public database more nearly current with our production data. We currently add annotated images to the production database at a rate of about 90 genes per month.

How does the image similarity search work?

This is custom image analysis software that uses representations of the expression patterns in virtual embryos generated with a deformable, triangular mesh grid. A full description of the method and related analysis tools are described in Frise et al., 2010. We are developing web versions of more of these image analysis tools and hope to add these as new features on this site in coming months.

How reliable are the annotations?

We make our best effort to produce accurate annotations, but we review annotations constantly and some may change with new data. Before the release of new experiments to the public website we check for any validating data, including microarray data, RNAseq data and literature. We appreciate input from the community. The annotation scheme and controlled vocabulary were developed with the help of Volker Hartenstein who continues to provide advice and has reviewed annotations for many of the genes. See his Atlas of Embryonic Development for more information, including the key to the color coding of our annotation terms.

Why are the embryo images not oriented so that anterior is to the left and dorsal to the top?

During the first phase of the project, including approximately the first 2000 genes, our microscopes were not equipped with a stage that rotated and we did not attempt to orient the embryos along the A/P and D/V axis, although we often rolled the embryos under the coverslip to be able to photograph the embryos from an angle that best reveals the staining pattern. We consider the images we capture raw, unprocessed data, not publication quality images. Once we acquired a microscope stage that can be rotated 360 degrees, we began to orient images with anterior to the left and dorsal up whenever possible. To facilitate automated image analysis, we reviewed our images and have added orientation tags using a custom web tool.

What probes to you use?

The detailed protocol for making the RNA probes we use is described in this Weiszmann et al., 2009. The templates we use are clones from the DGC collections and more recently, clones from the rapidly expanding Drosophila Gold Collection, with sequence verified full length ORFs. For high priority genes not yet represented in any of these collections, we make templates using either PCR from genomic DNA or RT-PCR from an appropriate RNA source.

Why do so many images show tracheal staining?

Tracheal staining is a common insitu artifact, although optimization of our hybridization protocol has significantly reduced this problem in more recent experiments. It is easily distinguishable from real tracheal staining, therefore if not annotated it should be considered artifactual.

What are the CRM reports shown for some genes?

We are adding embryonic expression patterns of reporter genes with expression driven by putative cis-regulatory modules (CRMs) near transcription factor (TF) genes to our database. These constructs are from the Janelia Farm CRM collection (Pfeiffer et al., 2008). Expression is detected using a probe to the GAL4 reporter RNA. Experiments for CRMs associated with a TF appear as additional experiments (CRM reports) on the gene report page after the wild type TF expression pattern experiments, with a link to the FlyBase sequence feature reports containing detailed descriptions of each CRM construct. The quick search function now includes CRM search terms. For the Janelia Farm CRM experiments, the experiment ID (EST ID) is the name shown in the FlyBase sequence feature table (e.g. GMR10D06, sequence feature FBsf0000161636). The CRM experiments are further distinguished from the wild type experiments by a different background color in the CRM reports. We have completed experiments for over 245 constructs and will be uploading these images to the database over the next few weeks. Experiments for additional CRMs (~800) are in production and will be uploaded to the database as the imaging is completed.

What are the images on top and the bottom of the homepage?

It is The Amazing Embryo Roulette. The links are randomly generated and will change every time you reload the page.

How should the data be cited?

Please cite the Berkeley Drosophila Genome Project and the following publications:

• Hammonds AS, Bristow CA, Fisher WW, Weiszmann R, et al. Spatial expression of transcription factors in Drosophila embryonic organ development. Genome Biol. 2013;14(12):R140. PMCID: not yet assigned
  http://www.ncbi.nlm.nih.gov/pubmed/24359758
• Tomancak P, Beaton A, Weiszmann R, Kwan E, Shu S, Lewis SE, et al. Systematic determination of patterns of gene expression during Drosophila embryogenesis. Genome Biol. 2002;3(12):RESEARCH0088. PMCID: 151190
  http://www.ncbi.nlm.nih.gov/pubmed/17645804
• Tomancak P, Berman BP, Beaton A, Weiszmann R, Kwan E, Hartenstein V, et al. Global analysis of patterns of gene expression during Drosophila embryogenesis. Genome Biol. 2007;8(7):R145. PMCID: 2323238
  http://www.ncbi.nlm.nih.gov/pubmed/12537577.

Other references:

• Frise et al., 2010, Systematic image-driven analysis of the spatial Drosophila embryonic expression landscape, Molecular Systems Biology 6:345
  http://www.ncbi.nlm.nih.gov/pubmed/20087342.
• Weiszmann R, et al. 2009, Determination of gene expression patterns using high-throughput RNA in situ hybridization to whole-mount Drosophila embryos, Nat Protoc. 4(5):605-18 (PMCID: PMC2780369)
  http://www.ncbi.nlm.nih.gov/pubmed/19360017.
• Mace DL, Varnado N, Zhang W, Frise E, Ohler U. 2010 Extraction and comparison of gene expression patterns from 2D RNA in situ hybridization images. Bioinformatics 2010
  http://www.ncbi.nlm.nih.gov/pubmed/19942587.
• Fowlkes CC et al. A quantitative spatiotemporal atlas of gene expression in the Drosophila blastoderm. Cell. 2008 Apr 18;133:364-74.
  http://www.ncbi.nlm.nih.gov/pubmed/18423206.
• Xiao-yong Li et al. Transcription Factors Bind Thousands of Active and Inactive Regions in the Drosophila Blastoderm PLoS Biol. 2008 6(2): e27.
  http://www.ncbi.nlm.nih.gov/pubmed/18271625.
• Pfeiffer BD, Jenett A, Hammonds AS, Ngo TT, Misra S, et al. 2008. Tools for neuroanatomy and neurogenetics in Drosophila. Proc Natl Acad Sci 105(28):9715-20. PMCID: 2447866
  http://www.ncbi.nlm.nih.gov/pubmed/18621688.