GSM3682110: ATAC-seq_E16.5_Hnf4_ghet_Control; Mus musculus; ATAC-seq
Embryos were collected at E16.5, and the freshly harvested embryonic small intestine (caudal stomach to rostral caecum) was opened longitudinally with forceps, and cut into 1 cm pieces. Intestinal tissues were treated with pre-warmed 0.25% Trypsin for 8 min at 37°C on a vortex station (speed set between 6-7), neutralized with 10% FBS, and passed through a 70-μm cell strainer. Cells were stained with the anti-CD326 (EpCAM) magnetic microbeads antibody (Miltenyi Biotec, 130-105-958) for 40 min on ice. To obtain single magnetic antibody conjugated EpCAM positive epithelial cells, stained cells were passed through a 40-μm cell strainer and then collected over a MS column (Miltenyi Biotec, 130-042-201) in a magnetic field. 20,000 cells were used for ATAC-seq as described previously with slight modifications. Briefly, cells were resuspended in ice-cold lysis buffer (10 mM Tris, pH 7.4, 10 mM NaCl, 3 mM MgCl2, and 0.1% NP-40), and then centrifuged at 500 g for 10 min at 4°C. The isolated nuclei were incubated with Nextera Tn5 Transposase (Illumina FC-121-1030) at 37°C for 30 min. The transposed chromatin was purified with QIAquick PCR Purification Kit (QIAGEN). The transposed DNA was amplified using NEBNext High-Fidelity 2X PCR Master Mix (New England Biolabs), and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.
GEO Accession
GSM3682110