title: GSM4150525: Tregs_RNAseq_CAT3; Mus musculus; RNA-Seq
library_construction_protocol: ChIPseq: 1×107 CD25+YFP+ Tregs were FACS sorted from LN and SPL isolated CD4+ T cells (CD4+ T Cell Isolation Kit, mouse, 130-104-454, Miltenyi) of 10-12-week-old Foxp3YFP-Cre WT mice. ATACseq/RNAseq: For ATAC–seq, 5-10x104 YFP+CD25+ Tregs were FACS sorted from MACS-pre-purified CD4+ T cells (CD4+ T Cell Isolation Kit, mouse, 130-104-454, Miltenyi) isolated from LNs of Foxp3YFP-Cre Ctnnb1fl(ex3) and Foxp3YFP-Cre WT mice ChIPseq: Emmanuel, A.O. et al. TCF-1 and HEB cooperate to establish the epigenetic and transcription profiles of CD4(+)CD8(+) thymocytes. Nature immunology 19, 1366-1378 (2018)., ATACseq: Cells were centrifuged at 500g at 4°C for 5 min, washed with 1 x PBS, and centrifuged again. Cells were resuspended in lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, and 0.1% IGEPAL CA-630) and immediately centrifuged at 500 g at 4 °C for 10 min. Pellets were resuspended in transposition reaction buffer (25 μl 2× Tagment Buffer (FC-121-1030, Illumina), 2.5 μl Tagment DNA Enzyme, and 22.5 μl nuclease-free H2O) for 30 min at 37 °C. DNA was purified with a Qiagen MinElute Kit and amplified with Nextera PCR primers (Illumina Nextera Index Kit) and NEBNext PCR Master Mix (M0541, New England BioLabs). Amplified DNA was purified with a Qiagen PCR cleanup kit. Libraries were sequenced on a HiSeq 4000 sequencer at the University of Chicago Genomics Facility, RNAseq: Total RNA was isolated using the PicoPureTM RNA Isolation Kit (KIT0202, Arcturus) following the manufacturer's instructions. Libraries were generated and sequenced by the University of Chicago Genomics Facility.
attributes.tag: GEO Accession
attributes.value: GSM4150525