Extended Data Figure 1: RAP-MS recovers and enriches the majority of Xist RNA from mouse ES cells, and these cells can be efficiently labelled with SILAC.
From: The Xist lncRNA interacts directly with SHARP to silence transcription through HDAC3
a, RT-qPCR measuring the percentage of the total cellular Xist or 18S recovered after RAP-MS of Xist. Values are computed as the amount of each RNA in the elution divided by the amount of RNA in the starting (‘input’) lysate material. Error bars represent the standard error of the mean from 5 biological replicates. b, Enrichment of Xist after RAP-MS captures from pSM33 cells as measured by qPCR. Bars indicate RNA levels of Xist, 18S, and Oct4 after purification of Xist, normalized to RNA in input sample. Each bar represents the RNA levels of Xist, 18S, and Oct4 after purification of Xist, normalized to RNA in input sample, from 3 biological replicates. c, SILAC labelling efficiency of a representative culture of pSM33 mouse ES cells after 10 days of growth (3 cell passages) in SILAC medium. Peptides were analysed by mass spectrometry, and values indicate the fraction of identified peptides with heavy-label incorporation with different levels of peptide labelling (shown in bins).
