title: GSM3387042: ATACseq_2i_siCTRL_rep3; Mus musculus; ATAC-seq
library_construction_protocol: ATAC-seq experiments were performed in biological triplicates of mES cells grown in 2i or serum conditions. Cell pellets from 50,000 cells for each condition were freshly harvested 72 h after transfection with siRNAs against TIP5 or a control sequence. The tagmentation reaction was performed as described in Buenrostro et al. (2013) with minor adjustments of the protocol, using the Nextera DNA Library Prep Kit (Illumina) together with the barcoded primers from the Nextera Index Kit (Illumina). In brief, an additional size selection step was performed after the first 5 cycles of library amplification. For this, the PCR reaction was incubated with 0.6 x volume of Ampure XP beads (Beckman Coulter) for 5 min to allow binding of high molecular weight fragments. Beads  containing long DNA fragments were separated on a magnet and the supernatant containing only small DNA fragments below roughly 800 bp were cleaned up using MinElute PCR purification columns (Qiagen). All libraries were amplified for 12 cycles in total, visualized and quantified with a TapeStation2200 (Agilent), and sequenced on a Illumnina HiSeq4000 instrument obtaining 125 bp single-end reads.
attributes.tag: GEO Accession
attributes.value: GSM3387042