title: GSM5456280: IEC_LKO_rep0; Mus musculus; ATAC-seq
library_construction_protocol: Small intestines were isolated using EDTA, frozen on dry ice, and pellet was kept at -80C. The cell pellet was resuspended in 50 μl lysis buffer and then spun down 500 × g for 10 min at 4 °C. The nuclei pellet was resuspended into 50 μl transposition reaction mixture containing Tn5 transposase from Nextera DNA Library Prep Kit (Illumina) and incubated at 37 °C for 30 min. Then the transposase-associated DNA was purified using MinElute PCR purification kit (QIAGEN). To amplify the library, the DNA was first amplified for 5 cycles using indexing primer from Nextera kit and NEBNext High-Fidelity 2X PCR master mix. To reduce the PCR amplification bias, 5 μl of amplified DNA after the first 5 cycles was used to do qPCR of 20 cycles to decide the number of cycles for the second round of PCR. The total amplified DNA was size selected to fragments less than 800 bp using SPRI beads. Quantification of the ATAC-seq library was done with QuBit. The size of the pooled library was examined by TapeStation. Barcoded ATAC-seq libraries were pooled and paired end sequenced (sX75) on the Illumina NextSeq 500 using the High output V2.5 kit (Illumina Inc., San Diego, CA).