GSM4972788: RORgt-KO_1; Mus musculus; ATAC-seq
1) Small intestinal lamina propria cells were prepared and extracted via Collagenase VIII digestion.  2) Cells were MACS enriched (Miltenyi Biotec), then stained with antibodies targeting surface markers and submitted to high speed flow sorting (BD FACS Aria Fusion).  3) Sorted cells were lysed and their DNA was transposed in a reaction buffer containing Tagment DNA Buffer (ref 15027866, Nextera DNA Library Prep Kit, Illumina), Tagment DNA Enzyme 1  (ref 15027865, Nextera DNA Library Prep Kit, Illumina), digitonin (ref G944A, Promega).  4) Transposed DNA was purified using Qiagen MinElute Kit. Libraries were prepared according to the protocol developped by Buenrostro et al. 2013 (Nature Methods, vol.10 no.12). Briefly, transposed DNA fragments were amplified by PCR, libraries were cleaned up using Ampure beads, checked using a Bioanalyser instrument and validated by qPCR. Their concentration was measured by a qPCR-based method (KAPA Library Quantification Kit for Illumina Sequencing Platforms). ATAC-seq libraries were sequenced using a NextSeq 500/550 High Output Kit v2.5 (Illumina) using the Illumina NextSeq500 platform.
GEO Accession
GSM4972788