ATAC-seq from human colonocytes inoculated with microbiome from Ind3 for 2 hrs (replicate 1)
We lysed 50,000 cells for ATAC-seq libraries. We used the Illumina Nextera Index Kit (Cat #15055290) in the PCR enrichment step and the cells were not lysed with 0.1\% IGEPAL CA-630 before adding the transposase to begin the ATAC-seq protocol. Individual library fragment distributions were assessed on the Agilent Bioanalyzer and pooling proportions were determined using the qPCR Kapa library quantification kit (KAPA Biosystems). Library pools were run on the Illumina NextSeq 500 Desktop sequencer in the Luca/Pique-Regi laboratory. Barcoded libraries of ATAC-seq samples were pooled and sequenced in multiple sequencing runs for 130M 38bp PE reads (max: 159M, min: 105M).