ChIP-seq analysis of gene expression regulated by LSD1 in CD8+ T cells
ChIP-seq assay was performed with GSK- or Vehicle-treated CD8+ T cells to interrogate the genome-wide distribution of LSD1, H3K4me1, H3K4me2, H3K4me3, H3K27ac, and Pol II, and their alterations in response to LSD1 inhibition. Overall design: In vitro cultured CD8+ T cells were fixed in 1% formaldehyde for 10 min at RT on a shaker, followed by quenching in 125 mM glycine. Next, cells were washed twice with ice-cold PBS and lysed in sonication buffer, then sonicated to obtain DNA fragments mostly between 300-800 bp. Subsequent procedures were performed following the Epigenetics Protocols Database PROT-11 (https://www.epigenome-noe.net/researchtools/protocols.php.html). ChIP-seq libraries were prepared using the VAHTS Universal DNA Library Prep Kit (Vazyme, ND607-01) according to the manufacturer's instructions. Library concentrations were quantified by Qubit (Invitrogen) and mixed equally for sequencing at Novaseq 6000 (Illumina) to generate 150 bp paired-end reads or at DNBSEQ-T7 (MGI Tech) to generate 100 bp paired-end reads.