Assays

Global Chromatin Profiling (GCP) technology is a mass spectrometry-based assay to identify and quantify post-translational modifications on histone proteins from bulk chromatin (i.e. measuring changes in epigenetic marks on histones). Around 60 different combinations of histone modifications can be quantified on H3, with even more possible combinations on H4, H2A (including isoforms), and H2B...

Reverse-phase protein array (RPPA) is a high-throughput technology that performs protein assays on thousands of samples simultaneously that measure the levels of protein expression, as well as protein modifications such as phosphorylation. Protein lysates are arrayed as microspots on nitrocellulized coated glass slides and probed with highly specific antibodies that have been validated for RPPA...

216,105 transcriptional signatures of cellular perturbations constructed using the LINCS pilot phase L1000. The chemical perturbagen and individual shRNA signatures are created by aggregating (ie averaging) Level 4 data for biological replicates as defined by the signatures metadata. Only signatures designated to be reproducible and self-connected ("gold") by the Broad institute are represented...

The P100 assay is a mass spectrometry-based targeted phosphoproteomic assay that detects and quantifies a representative set of 96 phosphopeptide probes. Phosphopeptides are enriched via an automated protocol and then mixed with a set of isotopically-labeled internal standards that correspond to the analytes in the P100 assay. This mixture is introduced into a mass spectrometer using ultra-high...

RNA-seq is a Next Generation Sequencing platform that measures gene expression across the transcriptome. A population of RNA (total or fractionated, such as poly(A)+) is converted to a library of cDNA fragments with adaptors attached to one or both ends. Each molecule is then sequenced in a high-throughput manner to obtain short sequences from one end (single-end sequencing) or both ends (pair-end...