Excised peritoneal membranes were immediately frozen in liquid nitrogen and stored at −80°C until use. Tissues were diced and ground to a fine powder with intermittent addition of liquid nitrogen. Omni–assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) was performed as described (41 (link)). Briefly, 100,000 nuclei per sample were isolated using an iodixanol gradient, and ATAC-seq was performed according to the original protocol (42 (link)) using a Nextera DNA sample preparation kit (Illumina, FC-121-1030). After amplification, library DNA was isolated (Qiagen MinElute kit), size selected, and sequenced (Illumina HiSeq 4000).
Millrine D., Cardus Figueras A., Uceda Fernandez J., Andrews R., Szomolay B., Cossins B.C., Rice C.M., Li J., Tyrrell V.J., McLeod L., Holmans P., O’Donnell V.B., Taylor P.R., Turner S.J., Jenkins B.J., Jones G.W., Topley N., Williams N.M, & Jones S.A. (2023). Th1 Cells Alter the Inflammatory Signature of IL-6 by Channeling STAT Transcription Factors to Alu-like Retroelements. The Journal of Immunology Author Choice, 211(2), 274-286.
Other organizations :
MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Medical Research Council, University of Bristol, Australian Regenerative Medicine Institute, Monash University, Hudson Institute of Medical Research, UK Dementia Research Institute
Excised peritoneal membranes were immediately frozen in liquid nitrogen and stored at −80°C until use.
Tissues were diced and ground to a fine powder with intermittent addition of liquid nitrogen.
100,000 nuclei per sample were isolated using an iodixanol gradient.
ATAC-seq was performed according to the original protocol (42 (link)) using a Nextera DNA sample preparation kit (Illumina, FC-121-1030).
After amplification, library DNA was isolated (Qiagen MinElute kit), size selected, and sequenced (Illumina HiSeq 4000).
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