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How to obtain LINCS metadata/column annotations associated with LDS-1191?
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20 months ago
Diwan • 560
United States


I am analyzing NIH LINCS gene expression data downloaded from: LINCS LDS1191

It is in .gctx file format and I am able to analyze the matrix. However, I am not able to obtain metadata/annotations associated with columns (i.e., chemical, dose, time). Each column has ids such as “CPC004_HEPG2_6H_X1_B5_DUO52HI53LO:K13”. Does anyone know how to get more information for these LINCS column ids?

It will be better if I can get the annotations associated with these column ids given by the LINCS group.

I am asking this because when I checked their GEO data (GSE70138), where they provided a small subset of data in a “.gct” format, I am able to obtain additional information like “SM_Dose”, “SM_LINCS_ID”, “SM_Time”, “SM_Pert_Type” etc.

Note: the above link also has a tab called metadata but provides only the basic information of chemical name, cell line name etc and not the exposure metadata.



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