GSM5592110: mRNAseq_IFNb_12h_Rep2; Homo sapiens; RNA-Seq
Samples 1-42: Cells were homogenized in TRIzol reagent and total RNA was extracted using the Direct-zol RNA Miniprep kit according to the manufacturer's instructions. Sample 43: Cells were trypsinized with 0.25% trypsin and collected as a single cells suspension. Cells were then washed twice with ice cold 1x PBS and filtered using a 40 μm Flowmi cell strainer (Bel-Art Scienceware). Cell count and viability were determined using trypan blue stain and a Countess II automatic cell counter (Thermfisher Scientific). Based on this cell count, a target cell input volume of 3,000 cells was loaded into a Chromium Controller using Chromium Next Gem (Gel Bead-In Emulsion) Single Cell 5' Library & Gel Bead Kit v1.1 (10x Genomics) according to manufacturer's instructions.. Samples 44-48: Cells were trypsinized and collected as a single cell suspension in complete DMEM. 50,000 cells were isolated and washed twice with ice cold PBS. Nuclei from washed cell pellets were extracted using lysis buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630). Transposition was performed at 37°C for 30 min using the Nextera DNA Library Prep Kit (Illumina) and transposed DNA was purified using the QIAgen MinElute PCR Purification kit according to the manufacturers' instructions. Samples 1-42: TruSeq Stranded mRNA Library Prep Kit (Illumina); Sampls 43: Chromium Single Cell 5' Library Kit v1.1 (10x Genomics); Samples 44-48: Nextera DNA Library Prep Kit (Illumina) Samples 1-42: RNA-seq; Sample 43: scRNA-seq; Samples 44-48: ATAC-seq