Quantification of gene expression by in situ hybridization: finding and using the raw values

I would like to know what the probe name used for the ISH experiments means in the Developing mouse brain atlas.
Some ISH done for the same gene at different developmental stages show different probe names. However, in some cases the sequence of the primers is the same but the probe number is not. If the primers used for the PCR were the same for generating 2 probes, the sequence of the probe should be the same, but in same cases they have a different number.
Thus, how do I know if the same probe was used for different experiments? What could be the differences between 2 probes with different probe number but generated with the same pair of primers?

Thank you for your help


Hi Juan,

The probe name, with the embedded date, indicates when the probe was made (“lot control”). The templateID indicates the probe design, so the sequence for a given templateID will always be the same. Hundreds of different probes could have been generated using the same templateID at different points in time, for different projects.

Thank you tylermo for the response about the probes names. Its very helpful

I was wondering about the status of the annotation of the P28 Development mouse brain atlas.
The Reference atlas does not show P28; however, saggital P28 experiments are shown for a number of genes. A query using RMA with the P28 section_IDs and structure unionize retrieves expression values. Do these values correspond to the annotation used for other postnatal stages? If so, what level of annotation show be considered for P28?

Thank you

To support quantification of data at P28, we registered the P56 annotation to the P28 reference space. Hence the level of annotation for P28 is the same as for P56 data.