What does individual RDS file name indicates?

[ZainulArifin1]

Hi. First of all, thank you for making this repository.

I noticed that the individual RDS file is named based on some identifier like LB, EST, and BCT. Do these identifiers refer to the cancer type?

[ncborcherding]

Hey Zainul,

Thanks for reaching out. The Sample ID was designed to try to convey information about the cancer, tissue type, patient ID,and sequencing run - if you have suggestions though, the repository has grown quite a bit.

In case you did not figure it out - you are correct, generally, the first 1-2 letters is the cancer and the last letter is the tissue type. So for example

• LB - is lung, blood, EST is Esophageal Tumor, BCT is basal cell tumor.
• The runs are labeled then with a numeric by the order of entry into the repository - for example, LT1.
• That LT1 may have associated samples such as normal lung tissue (which would be labeled as LN1 - keeping the same numerical samples).
• Multiple samples from the same patient will get a subdesignation - for example, the patient BCT1 had 5 sequencing runs BCT1.1-5 with specific cell isolation and treatment timepoints.

I will add the breakdown to the readme - that is my fault for not being clear.

Thanks, Nick