GSM9213565: monocytes_invitro_ATAC_rep3; Homo sapiens; ATAC-seq
To perform the RNA sequencing, total RNA was isolated using the RNeasy Tissue kit (Qiagen, Hilden, Germany, cat. 74104) according to the manufacturer's instructions. RNA was assessed for quality using an Agilent Tapestation 4200, and 50 ng of RNA with an RNA Integrity Number (RIN) greater than 8.0 were used to generate RNA sequencing libraries. RNA sequencing libraries using the Illumina Stranded mRNA Prep (Illumina) following manufacturer's instructions For ATAC-seq, live cells were rinsed with 1X PBS and lysed with cold 50 mL lysis buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630). After centrifugation at 500 x g for 10 min at 4°C, the resulting nuclei pellet was re-suspended in 50 mL tranposase reaction mix (Illumnia #20034197) and incubated at 37°C for 30 min. For ATAC-seq, Zymo ChIP DNA Clean and Concentrator-5 kit (Zymo Research D5205) was used to purify the DNA, which was then amplified with Nextera primers (1.25 M) using NebNext High-Fidelity 2X PCR Master Mix (New England Biolabs MO541). The final libraries were purified by gel excision of 155-250 bp fragments and single-end sequenced. For RNA sequencing libraries using the Illumina Stranded mRNA Prep (Illumina) following manufacturer's instructions