GSM9643605: RNA-seq of Th17 cells: Wild-type, biological replicate 2; Mus musculus; RNA-Seq
Total RNA was extracted from in vitro differentiated Th17 cells using TRIzol reagent (Invitrogen) according to the manufacturer's instructions. (RNA-seq);In vitro differentiated Th17 cells were crosslinked to fix protein-DNA interactions. Cell lysis, chromatin fragmentation, immunoprecipitation, and subsequent ChIP-DNA extraction and purification were performed using a ChIP assay kit from Cell Signaling Technology (CST) strictly following the manufacturer's instructions. (Chip-seq); Intact nuclei were isolated from fresh in vitro differentiated Th17 cells. Simultaneous chromatin fragmentation and adapter ligation (tagmentation), followed by DNA extraction and purification, were carried out using an ATAC-seq kit from Vazyme according to the manufacturer's protocol. (ATAC-seq); Fresh in vitro differentiated Th17 cells were harvested and bound to Concanavalin A (ConA) magnetic beads. Permeabilization, antibody incubation, targeted DNA cleavage by transposome, and final DNA extraction were performed using a CUT&Tag kit from Vazyme according to the manufacturer's instructions. (CUT&Tag-seq). RNA-seq libraries were prepared using the Illumina TruSeq RNA Sample Preparation Kit; For ATAC-seq and CUT&Tag-seq: Sequencing libraries were generated simultaneously during the tagmentation step and subsequently amplified by PCR using the respective Vazyme kits, following the manufacturer's instructions; For ChIP-seq: Sequencing libraries were constructed using Illumina TruSeq  according to the manufacturer's protocols.