title: GSM7114672: BC1_diff_rep2 [Capture-C]; Homo sapiens; OTHER
library_construction_protocol: HiC and Capture-C: Cells were fixed with 2% formaldehyde for 10 min at RT. Cells were lysed and homogenized before chromatin was digested with Arima enzyme cocktail. Capture-C: Cells were fixed with 2% formaldehyde for 10 min at RT. Cells were lysed and homogenized before chromatin was digested with DpnII. HiC and Capture-C: HiC was performed in iCell GlutaNeurons, and Capture-C was performed in iCell GlutaNeurons and GABANeurons. All experiments were performed in triplicate with independent cell grow-ups of approximately 15 million cells for biological replication. For HiC, we followed manufacturer recommendations from the Arima HiC kit- User Guide for Mammalian cell lines (A510008, V.Oct.2019) using the Arima HiC Library Prep using Swift Biosciences Accel-NGS 2S plus DNA library kit (A510008, V. Nov2018). iCell GlutaNeuron and GABANeuron Capture-C was performed following the HiC protocols, with the addition of the Agilent Technology SureSelect XT HS/SureSelect XT Low input target enrichment with pre-capture pooling protocol. 102 SureSelect DNA probes spanning a 2kb region (chr17:45892780-45893184 and chr17:45893527-45895196; hg38) were ordered from AgilentTechnologies. The region between the two probes could not be synthesized because of low sequence complexity. Capture-C: Capture-C was performed in NPCs, Day 14 BrainPhys differentiated neurons. All experiments were performed in triplicate with independent cell grow-ups of approximately 15 million cells for biological replication. NPC and Day 14 BrainPhys differentiated neuron Capture-C was performed following the NG Capture-C Protocol (v2.4).46 For this experiment, enrichment for MAPT promoter contacts was performed by double capture using two biotinylated oligonucleotides targeting chr17:45892836–45892923 and chr17:45895092–45895179 (both hg38)