Anti h3k4me1

ChIP-seq assays with two independent experiments if not stated otherwise on naïve CD4⁺ T cells were performed as described previously^{46 (link),47 (link)}. Briefly, cells for ChIP-seq were fixed for 10 min in 1% formaldehyde, sonicated and chromatin immunoprecipitation was performed with anti-MLL4^{19 (link),20 (link)}, anti-H3K27ac (Abcam; single experiment) and anti-H3K27me3 (07-449, Millipore) antibodies. ChIP-seq for H3K4me1 was performed on native (not fixed) chromatin with anti-H3K4me1 (ab8895, Abcam). ChIP DNA was end-repaired using an End-It DNA End-Repair kit (Epicentre), indexed, amplified and sequenced on an Illumina 2G Genome Analyzer.

ChIP-seq was performed using the ‘ChIPmentation’ approach^{59 (link)}. Briefly, H3K4me1, H3K27ac and H3K27me3 ChIP-seq experiments were performed on 200,000 FACS-sorted bulge-SCs from mice. Cells were cross-linked in 1% (wt/vol) formaldehyde fixation buffer, resuspended and lysed. To solubilize and shear cross-linked DNAs, lysates were subjected to a Covaris S220 focused ultrasonicator (140 PIP, 5% duty factor, 200 CPB, and 4°C). The resulting whole-cell extract was incubated overnight at 4^oC with 4μL of Dynabeads Protein G magnetic beads (Life Technologies), which had been pre-incubated with 2ug of anti-H3K4me1 (Abcam Cat#ab8895), anti-H3K27ac (Abcam, Cat#ab4729) or anti-H3K27me3 (Millipore, Cat#07–449) antibodies. After chromatin immunoprecipitation, samples were washed, and tagmentation reaction was performed on beads using Nextera DNA sample preparation kit (Illumina). After several washes, bound complexes were eluted and reverse–cross-linked. ChIP DNA was prepared for sequencing by PCR using Illumina barcoded primer sets. After amplification, a range of fragment sizes between 300–700bp was selected using AmpureXP beads purification. Sequencing was performed on the Illumina Nextseq500 Sequencer using a 38/37bp paired-end high-output mode setting.