1. What can I get from Phenics?

    Phenics provides access to quantitative values on cell division timing and tissue marker expression for each cell at one and a half minute interval during development of wild type or perturbed embryos. Despite a wild type embryo develops into 550 cells, only the data prior to 350 cell-stage are reliable because a cutoff of approximately 350 cells is set for curation of output of automated lineaging. In the case of some RNAi treated animals, its embryo may not develop up to the 350-cell stage. Therefore, the cellular and expression data wil be reliable up to the last available time point for curation which is indicated for each movie.

    In addition to the raw data on cell division timing and marker expression, pairwise comparison of division timings between wild type and the RNAi embryos is precomputed and presented as various formats, including side-by-side scatter plot of overall cell division timing, side-by-side comparison of cell division timing between individual cells with net differences shown explicitly as histogram or horizontal bars. Overall developmental speed (overall cell count plotted against time) is presented side-by-side between 91 wild type and a single RNAi embryos. A lineage tree with superimposed marker expression can be visualized online or downloaded as PNG file.

    A 3D projection movie showing cell migrations is also precomputed from the ourput of lineaging pipeline and presentated as online playable MP4 format. The movie can also be downloaded for local use by right-click. Founder cells and its descendants are color coded as below the movie. The movie was tested with web browser Firefox and Internet Explorer, but not thoroughly with Safari for which some issues were encountered with certain version.

Organization of "Phenics" database

Flowchart of data analysis

flow

2. How can I get what I want?

    Click tab "RNAi knockdown" to asscess the data on curated movies and those that cannot be uncurated due to early embryonic arrest (See figure above). Most data are stored under curated movies where the detailed information on cell divsion timing, cell lineage, 3D projection of nuclei as well as pairwise comparison of division timing between perturbed and wild type embryos. Link to the external databases, Wormbase and UCSC genome browser is available for detailed information on individual gene and RNAi targeting region. For uncurated movies, only the terminal phenotypes of arrested embryo are given.

    The data are searchable by gene name, experiment name, number of editable cell etc. It can also be sorted by these item as well by clicking each item. Users can input one or more key words in the blank searching area at one time to retrieve the item contaning the words. For example, if users input "PHA" in the blank below "Marker gene", and "cbp" in the blank below "KO gene", the RNAi relicates which use PHA-4 for Marker and knock out genes containing "cbp" will be presented.

    Click tab "Division timing" to asscess the data on pre-computed division timings (in minute) for each individual cells or DDT (differences in division timing) between sister cells for all wild type and perturbed embryos. Query for gene specific data can be performed in the similar way as that for RNAi knockdown.

   Click tab "Marker expression" to asscess the data on pre-computed expression intensity with one value for each cell for all wild type and perturbed embryos. Query for gene specific data can be performed in the similar way as that for RNAi knockdown.

3. Terminology used in the database

Column Description
Experiment name The unique identifier for each RNAi replicate, starting with the dsRNA injection date (year(first two digits)-month-day), tissue marker gene, RNAi targeted gene, and imaged embryos as replicate.
Click the identifier to access more details of the experiment.
Lineaging strain The C. elegans strain that is used in automated lineaging.
Marker gene The tissue-specific marker gene used for marking cell fate. In most cases, PHA-4 and NHR-25 were used.
KO gene The gene targeted by RNAi.
Click the gene to view more details on WormBase.
Edited cell number The count of cells up to the last editted time point.
Edited time point The last time point a movie is editted.
Left Primer The sequences of left primer used for synthesis of dsRNA for the corresponding gene.
Right Primer The sequences of right primer used for synthesis of dsRNA for the corresponding gene.
Primer Coordinate The chromosome coordinates of primer used for synthesis of dsRNA for the corresponding gene.
Click the coordinate to view the PCR sequence and gene annotation on UCSC genome browser.
Scatter Plot of Cell Division Timing between RNAi and wild type embryos The scatterplot for cell division time comparison.
Histogram of side-by-side comparison of Division Timing between RNAi and wild type Histogram cell division time comparison, with difference labeled.
Pairwise comparison of Division Timing for individual cell Plot of cell division time comparison, with difference labeled, seperated by lineages.
Developmental Speed Plot of cell count over developing time in minute.
Lineage Tree Embryonic cell lineage (blue) superimposed with tissue marker expression (red).