GSM9670759: Knockout 1; Mus musculus; ATAC-seq
Prior to analysis, CD74+/+- and CD74-/--derived mBMDMs under LPS stimulation were processed for ATAC-seq profiling using the Hyperactive ATAC-Seq Library Prep Kit for Illumina (Vazyme #TD711) following manufacturer specifications. Nuclear isolation was achieved through hypotonic lysis coupled with density gradient centrifugation. Isolated nuclei underwent Tn5 transposase-mediated fragmentation and adapter ligation with dual-indexed adapters from the TruePrep Index Kit V3 for Illumina (Vazyme #TD203) to simultaneously tag open chromatin regions and incorporate unique molecular identifiers. Transposed DNA fragments were amplified via limited-cycle PCR using kit-supplied reagents, followed by purification through magnetic bead-based size selection to construct sequencing-optimized libraries Library quality assurance included fragment distribution analysis (Agilent Bioanalyzer), fluorometric quantification (Qubit 4.0), and diversity assessment via qPCR. Qualified libraries were sequenced on an Illumina HiSeq4000 system, generating raw data for subsequent computational processing.