Normalizing Protein Expression Data

Raw data was exported using GeoMx DSP sopware to normalize the digital counts using internal spike-in controls (ERCCs) and scale each AOIs to area. All batch control, post-normalizaAon, staAsAcal analysis, and differenAally expressed protein (DEP) data visualizaAon were performed using R sopware (ver. 4.3.1, R FoundaAon for StaAsAcal CompuAng, Vienna, Austria, hFps://www.R-project.org/).

Partial Protocol Preview
This section provides a glimpse into the protocol.
The remaining content is hidden due to licensing restrictions, but the full text is available at the following link: Access Free Full Text.

Son G., Mladinov M., Pereira F.L., Li S.H., Tu C., Judge G., Yang Y., Suemoto C.K., Leite R.E.P., Paes V.R., Pasqualucci C.A., Filho W.J., Spina S., Seeley W.W., Chang W., Neylan T.C., & Grinberg L.T. (2024). Spatially conserved pathoprotein profiling in the human suprachiasmatic nucleus in progressive Alzheimer disease stages.

Publication 2024

Corresponding Organization : Universidade de São Paulo

Other organizations : San Francisco VA Medical Center

Top 5 similar protocols

Variable analysis

independent variables

Independent variables not explicitly mentioned.

dependent variables

Dependent variables not explicitly mentioned.

control variables

Control variables not explicitly mentioned.

controls

The authors mention using internal spike-in controls (ERCCs) to normalize the digital counts.

Annotations

Based on most similar protocols

Etiam vel ipsum. Morbi facilisis vestibulum nisl. Praesent cursus laoreet felis. Integer adipiscing pretium orci. Nulla facilisi. Quisque posuere bibendum purus. Nulla quam mauris, cursus eget, convallis ac, molestie non, enim. Aliquam congue. Quisque sagittis nonummy sapien. Proin molestie sem vitae urna. Maecenas lorem.

As authors may omit details in methods from publication, our AI will look for missing critical information across the 5 most similar protocols.

About PubCompare

Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.

We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.

However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.

Ready to get started?

Revolutionizing how scientists
search and build protocols!