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ATAC sequencing

XG Xiangyu Ge
MF Mojca Frank-Bertoncelj
KK Kerstin Klein
AM Amanda McGovern
TK Tadeja Kuret
MH Miranda Houtman
BB Blaž Burja
RM Raphael Micheroli
CS Chenfu Shi
MM Miriam Marks
AF Andrew Filer
CB Christopher D. Buckley
GO Gisela Orozco
OD Oliver Distler
AM Andrew P. Morris
PM Paul Martin
SE Stephen Eyre
CO Caroline Ospelt
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Cultured RA FLS were stimulated with 10 ng/ml TNF for 24 h or were left untreated (Additional file 2: Table S2). From each patient cell line, 50'000 cells were prepared according to the protocol by Buenrostro et al [76]. ATAC-seq libraries were sequenced on Illumina HiSeq 4000 with 75 bp paired end reads. The reads were QC’d with FastQC for read quality, and the Nextera-transposase adaptors were trimmed with cutadapt [77]. The reads were aligned with Bowtie 2 to the GRCh38 human reference. PCR duplicates were identified and removed by Picard Tools prior to peak calling using MACS2 [78]. Both broad and narrow peaks were called as ATAC-seq can have properties of both.

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