Analysis of transcription factor binding on nucleosomal DNA

We developed NCAP–SELEX (nucleosome consecutive affinity purification–systematic evolution of ligands by exponential enrichment), to address the modes of interactions between transcription factors (TFs) and nucleosomal DNA. Here are the reads that support the findings reported in Zhu et al., Nature 2018. The filename of the reads consists of multiple fields separated by double underscores "__". All fields describe experimental conditions. Importantly, the first field indicates the experiment type, with possible values including: 1. “NCAP-SELEX”: Main set of NCAP-SELEX experiments. For each TF, there are forward (R1) and reverse (R2) reads for cycles 1 to 4. At cycle 5, both nucleosome bound and unbound DNA is sequenced, in presence or absence of TF. Ligand used is indicated by either “lig200” or “lig147”. 2. “Doubled_TFconc”, the NCAP-SELEX and dissociation assays under doubled TF concentrations. 3. “Linker-Region”, NCAP-SELEX using a ligand containing randomized nucleosome linker regions. 4. “HT-SELEX”, high-throughput SELEX run with TFs in the absence of nucleosome 5. “Nucleosome-SELEX”, nucleosome-SELEX without TFs to determine the sequence preferences of the nucleosome, including both the nucleosome-favored (bound) and nucleosome-disfavored (unbound) libraries. 6. Empty (filenames begin with "__"). Unselected input library reads (“cycle 0”). 7. “Competition_assay”, assays comparing RFX5's affinity to free and nucleosomal DNA. 8. “Lig200-MNase”, investigating nucleosome positions on lig200 by MNase digestion. 9. “Liver_NuExt”, the active TF identification (Wei et al., Nat. Biotechnol., 2018) experiments using mouse liver nuclear extract, validating the periodic preference of homeodomain TFs. 10. “MNase-ChIP”, MNase-ChIP experiments for RFX5 and HOXB13 expressed in HEK293 cells. 11. “MNase-seq”, MNase-seq for LoVo cells and HEK293 cells. The MNase-seq of HEK293 after the TF expression also represents the input of MNase-ChIP. Most reads are sequenced in paired-end, thus the field “PEread” can be either R1 or R2. For SELEX-related experiments, the main fields include “ligand” (ligand design used in SELEX), “TF” (the TF used in SELEX), “cycle” (the selection cycle of SELEX), “batch” (the batch of experiment run), “well” (the position of sample in the multi-well plate)