title: GSM8301049: neuron_NMDA_rep3_ssRNase_protein; Rattus norvegicus; OTHER
library_construction_protocol: Control- and NMDA-treated cells collected and resuspended in Lysis buffer PIP-seq libraries were constructed as previously described (Kramer and Gregory, 2019). To summarize, INTACT purified nuclei from 3 grams of tissue per replicate were lysed and separated into footprinting and structure-only samples. The footprinting samples were then treated with either dsRNase (ds-P) or ssRNase (ss-P) before protein digestion by proteinase K and reversal of crosslinks. In the structure-only samples, proteins were first digested with proteinase K before treatment with either dsRNase (P-ds) or ssRNase (P-ss). Each sample resulted in 4 libraries: 2 footprinting libraries (ss-P, ds-P) and 2 structure-only libraries (P-ss, P-ds). All libraries were sequenced on an Illumina HiSeq2000 using the standard protocol for 50 base pair single read sequencing.