Hello,
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?
The probe name, with the embedded date, indicates when the probe was made (ālot controlā). 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?
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.
Hello,
Thank you for all previous answers!
Iām trying to find the connectivity values between the isocortex and the subpallium. This data was published in as a low resolution matrix heatmap in Fig 3 of the Oh et al 2014 Nature paper, which refers to a supplementary table for the raw values. However, I couldnāt find the supplementary table. I was wondering if someone has access to a higher resolution figure of the connectivity values between each structure of the isocortex and the subpallium.
Thank you for your help
I was wondering is there is a way to access gene expression data (by RNAseq or microarrays) in anatomical regions of the mouse CNS (adult or developmental).
I would like to compare the data from ISH with gene expression data obtained by other techniques.
I extracted ISH data using the StructureUnionize model, but I could use more gross anatomical structures.
If ABA does not have this type of data, are you aware of other sources that analyze gene expression in specific mouse CNS areas?
There is no bulk tissue microarray or RNA-seq data as part of the Allen Mouse Brain Atlas. The only data set I know of that may be of some relevance is a microarray study from 2004. There are almost definitely more recent, higher resolution data sets that others might be able to provide.
Following on from my original questions at the start of this topic:
Iād like to make a link to a pre-print that weāve just released in which I describe the ISH expression reverse engineering that I applied to Allen Developing Mouse Brain Atlas data. See Figure S1 in the pre-print. There is also Octave (like MATLAB) and Python code in a related repository to show exactly what I did.
In that work, we demonstrate, and describe our new tool, Stalefish, which allows us to create 3D gene expression surfaces from sets of 2D ISH expression data, such as those found in the Allen Developing Mouse Brain Atlas. What makes our technique and software useful is that it is very easy to integrate with your standard workflow for producing ISH slices - you donāt need the significantly complex techniques employed by the Allen project; you can apply the technique to your existing slice images, although you will get the best results if you use a needle to make an alignment mark when fixing your brains.
Just a short question related to this.
I was trying to get the heatmap of a gene called Efnb2 during development.
I modified the syntax found in the API Manual.