The samples were selected from PDX digested cell lines cultured under various growth conditions. Two parameters are defined in the sample sheet. The "sample ID" column represents the cell lines we froze at passage 2, indicating successful adaptation to their media condition. After thawing these lines, we cultured them for 7 days in a new media condition, as indicated by the "condition" column.
Why we use two alignment method
In our procedures, we have established two different versions of the counting matrix, each using a different alignment method. These versions have been created for the purpose of comparison, accuracy, and for specific study purposes.
The first version is named JT version_Salmon. This version uses the Salmon method for alignment. Salmon is a versatile tool capable of quantifying transcript expression. This method allows for precise alignment and is particularly useful in our previous PDX tissue process.
The second version is the NA (from Dr. Auslander) version_STAR. This version uses the STAR method for alignment. STAR is an advanced method that utilizes a high-throughput sequencing aligner. It's known for its speed and accuracy, making it a reliable tool in our methodology. The NA version_STAR has been used in our research to study drug predictions.
<aside> 💡 Please be aware there are some genes were not observed in current sheet due to threshold applied on alignment. The update version will be updated shortly.
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