title: GSM3460556: ATAC-Seq_rep2; Mus musculus; ATAC-seq
library_construction_protocol: The ATAC-Seq was performed using 50,000 c-Kit+CD144+ CD45.2- cells isolated from AGM region of E11.5 wild-type B6 mouse embryos. The Tn5 transposome was purified and assembled following a published protocol (46).  The permeabilization was performed with 50 µl cold ATAC-RSB buffer (0.1% NP40, 0.1% Tween-20, and 0.01% Digitonin) and the transposition was performed with 50 µl transposition mix (10µl 5× HEPES DMF Buffer, 3 µl 5 µM Tn5 transposome, 37 µl PBS, 0.5 µl 10% Tween-20, and 0.5 µl 1% digitonin) and incubated at 37° for 30 min. After transposition, the cleaned-up DNA fragments were pre-amplified for 5 cycles using NEB Q5 master mix. Each reaction contains 2.5 µl of 25 µM i5 primer, 2.5 µl of 25 µM i7 primer, 25 µl 2× NEB Q5 master mix, and 20 µl cleaned up samples.  PCR settings were 5 min at 72°C, 30 sec at 98°C, and followed by additional 5 cycles (98°C for 10 sec, 63°C for 30 sec, 72°C for 1 min). After pre-amplification, 1 µl of the pre-amplified mixture was used to run a 10 µl qPCR test to determine the optimal amplification cycle. The final amplified DNA library was purified using Qiagen DNA purification kit.