I'm working with a [LINCS L1000 dataset][1] 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!


  [1]: http://lincsportal.ccs.miami.edu/datasets/#/view/LDS-1203
To answer my own question.

The column ids for Level 3 and Level 4 data is basically the distil_id. The example I posted 

LJP001_BT20_24H_X1_B2_DUO52HI53LO:A03

can be broken into 

 - the perturbagen group "LJP001"
 - the cell line "BT20"
 - the brew prefix "LJP001_BT20_24H"
 - the plate index "X1_B2_DUO52HI53LO"
 - the well index "A03"
 - the distil_id "LJP001_BT20_24H_X1_B2_DUO52HI53LO_A03" (note the switch from ':' to '_')

It turns out that the distil_id doesn't contain enough information to identify the perturbagen used. To identify this, you need to use the [LINCS api][1]. Here is [more information][2] about using the LINCS api to query the metadata. I also used [this Coursera video][3] as a reference. Note that the example given in the question doesn't work with the API.


  [1]: http://api.lincscloud.org/a2/docs/instinfo
  [2]: http://support.lincscloud.org/hc/en-us/articles/202107633-Metadata-Getting-Lists-of-Perturbagens-Cell-Lines-Cell-Types
  [3]: https://www.coursera.org/learn/bd2k-lincs/lecture/grLin/introduction-to-lincs-l1000-data