GSM5140782: HepaRG_ChIP_H3K4me3_3D_rep1; Homo sapiens; ChIP-Seq
For RNA-Seq, total RNA of HepaRG in 2D and 3D-PEG culture was extracted using TRIzol (Invitrogen, USA). For ChIP-seq and BL-Hi-C, HepaRG cells in 2D and 3D-PEG culture (~1x106 cells/repeat) were collected in basal medium and crosslinked using 1 % formaldehyde (Sigma). For ChIP-Seq, Fixed cells were treated by lysis buffer containing 1 % sodium dodecyl sulfate (SDS, Invitrogen) and cOmplete ULTRA Tablets (Roche, USA) for 10 min at 4 oC. Then chromatin was fragmented by ultra-sonication processor (Cole-Parmer, USA) on ice. Fragmented chromatin was captured using ChIP-grade antibody (2 μg/sample) and DynabeadsTM Protein G (ThermoFisher, USA) for overnight at 4oC. Enriched chromatin fragments were treated with proteinase K (Sigma) and extracted DNA using dynabeads (Vazyme, China). For BL-Hi-C, after fixation and lysis, cells were treated with HaeIII enzyme (NEB, USA) and processed to the two-step ligation with biotin modified bridge linker. For ATAC-Seq, HepaRG cells in 2D and 3D-PEG culture on day 5 (~5x104 cells/repeat) were collected and treated with cold lysis buffer containing 10 mM Tris·HCl, 10 mM NaCl, 3 mM MgCl2, and 0.1% IGEPAL CA630 (Sigma) for 10 min on ice. For ChIP-seq/BL-Hi-C/ATAC-Seq, extracted DNA were processed to construct libraries using TruePrep DNA library Prep Kit (Vazyme) according to manufacturer's instruction For ChIP-Seq/ATAC-Seq: 5'-AATGATACGGCGACCACCGAGATCTACACXXXXXXXXTCGTCGGCAGCGTCAGATGTGTATAAGAGACAG-NNNNNN-CTGTCTCTTATACACATCTCCGAGCCCACGAGACIIIIIIIIATCTCGTATGCCGTCTTCTGCTTG-3'  For BL-Hi-C: 5'AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-NNNNNN-AGATCGGAAGAGCACACGTCTGAACTCCAGTCACIIIIIIII7ATCTCGTATGCCGTCTTCTGCTTG3'