title: GSM8625659: popliteal_inflamed_rep2; Mus musculus; ATAC-seq
library_construction_protocol: ATAC-seq was performed according to a published Omni-ATAC protocol. 5-8x103 sorted lymph node FRCs from popliteal or brachial lymph nodes were centrifuged at 500 r.c.f. for 5 min at 4°C in a fixed-angle centrifuge. Cell pellets were lysed and tagmented in one step by resuspending in 25 ul of tagmentation reaction mix containing 0.02% digitonin, 0.1% Tween-20, and 100 nM Tn5 transposase in tagmentation buffer (10 mM Tris-HCl, 5 mM MgCl2, and 10% dimethyl formamide). Transposition reactions were incubated at 37 °C for 60 min in a thermocycler. Reactions were cleaned up with Zymo DNA Clean and Concentrator 5 columns (Zymo Research). ATAC-seq libraries were prepared following the protocol described in Buenrostro et al., 2015. A series of SPRI-bead size selections were performed to generate libraries with a target library size between 300-400bp which primarily represents sub-nucleosomal and mono-nucleosomal peaks. Library concentrations were determined using UV Qubit fluorometer. Libraries size distributions were validated using the Agilent High Sensitivity DNA kit.