ESCs were crosslinked with formaldehyde, lysed, immunoprecipitated, washed, and reverse crosslinked. RNA was hybridized to the Nanostring codeset. We tested antibodies for 28 chromatin complexes and selected successful antibodies that (i) had >10 lincRNAs exceeding a 5-fold change and (ii) had significant enrichments across 3 replicates. We compared the overlap in gene expression using a modified GSEA34.
