Getting Started with LINCS Datasets and Tools

Abstract The Library of Integrated Network‐based Cellular Signatures (LINCS) was an NIH Common Fund program that aimed to expand our knowledge about human cellular responses to chemical, genetic, and microenvironment perturbations. Responses to perturbations were measured by transcriptomics, proteomics, cellular imaging, and other high content assays. The second phase of the LINCS program, which lasted 7 years, involved the engagement of six data and signature generation centers (DSGCs) and one data coordination and integration center (DCIC). The DSGCs and the DCIC developed several digital resources, including tools, databases, and workflows that aim to facilitate the use of the LINCS data and integrate this data with other publicly available data. The digital resources developed by the DSGCs and the DCIC can be used to gain new biological and pharmacological insights that can lead to the development of novel therapeutics. This protocol provides step‐by‐step instructions for processing the LINCS data into signatures, and utilizing the digital resources developed by the LINCS consortia for hypothesis generation and knowledge discovery. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1 : Navigating L1000 tools and data in CLUE.io Basic Protocol 2 : Computing signatures from the L1000 data with the CD method Basic Protocol 3 : Analyzing lists of differentially expressed genes and querying them against the L1000 data with BioJupies and the Bulk RNA‐seq Appyter Basic Protocol 4 : Utilizing the L1000FWD resource for drug discovery Basic Protocol 5 : KINOMEscan and the KINOMEscan Appyter Basic Protocol 6 : LINCS P100 and GCP Proteomics Assays Basic Protocol 7 : The LINCS Joint Project (LJP) Basic Protocol 8 : The LINCS Data Portals and SigCom LINCS Basic Protocol 9 : Creating and analyzing signatures with iLINCS