Frequently Asked Questions

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

We very often roll the embryos under the coverslip to be able to photograph the embryos from an angle that best reveals the staining pattern. Initially we did not attempt to orient the embryos along the A/P and D/V axis. We consider the images we capture raw, unprocessed data not publication quality images. Since majority of Drosophila researchers find it difficult to examine un-oriented embryos, we recently acquired a microscope stage that can be rotated 360 degrees so that the images that we capture from now on are going to be oriented at least along the anterior posterior axis. We are considering orienting the embryos retrospectively.

When is the dataset going to be finished?

There is no simple answer to that question. The project started more than a year ago, however there has been a substantial period of optimization of the pipeline. Recently we achieved a steady production rate of one to two 96-well plates a week. If no unforeseeable circumstances occur we should be able to finish the first pass through the EST collections within a year. After that we will attempt to redo the failures.

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What about the genes with no ESTs?

Currently no specific plans about those. More ESTs are going to be available in the future or probes may be produced by RT-PCR.

How often is the dataset updated?

Data are going to be released every three months, so that there is no need to regularly check the website for new arrivals.

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�� Are you going to expand the project to other tissues?

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We are considering using our probes on other tissues such as imaginal discs or ovaries. We are currently working out the mass isolation and 96-well staining protocol for those tissues.

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�� How reliable is the annotation?

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Annotation should be considered work in progress. All annotations are performed during image capture stage of the project and are performed by single person (Amy Beaton) ensuring internal consistency. Unbiased annotation of development of gene expression patterns in all major embryonic systems is a formidable task. Users should be aware that the dataset reflects the learning curve of the annotator. Generally in earlier stages of the project expression was assigned to various structures rather generously and therefore results of the searches may represent the superset of the genes positively expressed in a particular tissue. Moreover the controlled vocabularies for annotation are still developing. We plan to curate and improve the annotation continually with the help from Volker Hartenstein. We welcome all comments and suggestions on the annotation effort. ��

�� Why do so many images show tracheal staining?

Tracheal staining is a common insitu artifact. It is easily distinguishable from real tracheal staining, therefore if not annotated it should be considered artifactual.

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�� What are the notes and comments on the insitu report pages?

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We generally do not take images of ubiquitous or maternal only staining. Notes contain stage specific controlled vocabulary terms to describe those situations (maternal, ubiquitous), indicate absence of staining (no staining), or some kind of problem (junk, production problem). Comments are very important; they contain free text messages that address issues on the staining pattern that cannot be captured with the current controlled vocabularies. This system is a relic from pilot project pipeline and will be changed soon.

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?

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We are currently preparing a manuscript describing the insitu production pipeline, annotation effort and results of analysis of expression patterns for 1/5 of Drosophila genes during embryogenesis (P. Tomancak et.al. http://genomebiology.com/2002/3/12/research/0088.1).

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