I'm working with a LINCS L1000 dataset that gives the GE of a cell line before and after perturbation by a small molecule. I am using Level 4 data. After loading the .gct file into matlab, I get a matrix of 22268-by-40172 as well as a vector of column_ids and a vector of row_ids.
Using the row ids and the gene metadata txt file included in the download, I know that each row represents a gene.
I can't figure out what a column represents. Obviously, each columns is a single experiment but I can't understand what each id means.
For example, here is a column id "LJP001_BT20_24H_X1_B2_DUO52HI53LO:A03".
So far, I know that "LJP001" refers to LINCS Joint Project and "BT20" refers to the specific cell line. Somewhere, it must contain information about the small molecule used as a pertubagen but I don't know how to interpret this. Any help would be greatly appreciated!