The detailed view in the cell line atlas shows images of the immunostained cell line chosen. Staining and automatic annotation is done for duplicate samples for each antibody. The area/cells buttons can be used to mark the areas and cells that have been detected. The assay and annotation is described here.

By clicking on an image, an enlarged view of that image will open. The area and cell overlay images can be visualised and the image can be panned.

Below the images detailed information on image analysis results is displayed as antibody staining, staining intensity, the number of cells identified in the image as well as the fraction of immunopositive cells.

The RNAseq details section shows detailed information about the individual samples used for the transcript profiling and results of the RNAseq analysis.

On top the transcript layout for all coding and non-coding transcripts of the gene, with introns scaled down by a factor 20, is shown. Untranslated regions (UTRs) of protein-coding transcripts are colored gray.

FPKM (Fragments Per Kilobase of exon per Million fragments mapped) values give a quantification of the gene abundance which is comparable between different genes and samples. The FPKM is calculated as the sum of FPKMs of all protein-coding transcripts.

The plots show the mapped read coverage along all exons and introns of the gene, thereby revealing which exons are expressed and at what relative levels. The levels are normalized by total library size and scaled to fit the highest peak of all samples to the height of the plot. Thus these plots should not be used to compare abundances between different samples or genes, but rather as an indication of which transcripts are expressed and as a quality control.