title: GSM4121481: stage 12 ectodermal explant rep1; Xenopus laevis; ATAC-seq
library_construction_protocol: Xenopus laevis ectodermal explants (animal caps) were dissected at the blastula stage and collected at the onset of gastrulation (stage 10) or at the end of gastrulation (stage 12). Two explants per replicate were washed twice in 1 ml cold PBS, resuspended in 50 µl RSB (10mM Tris pH 7.4, 10mM NaCl, 3mM MgCl2) with 0.1% (v/v) Igepal CA-630 at 4ºC and dispersed by pipetting. Samples were centrifuged at 500xg for 10 minutes at 4ºC, and pellets were resuspended in 1X TD buffer (10mM Tris pH 7.6, 5 mM MgCl2, and 10% dimethylformamide) and 2.5µL of Tn5 (3µM) was added. Samples were incubated at 37ºC for 1 hour with constant shaking and digested with protease K overnight. DNA was purified with 1.8 volumes of Ampure XP Beads (Beckman Coulter), eluted in 40 µl, amplified by PCR with barcoded primers as described (Buenrostro et al., 2013), purified by AMPure XP beads (Thermo-Fisher) to remove adaptors, and submitted in triplicate for sequencing on a HiSeq 4000 with 100 nucleotide paired-end reads. Libraries were constructed using the Illumina Nextera Library Prep kit (cat#15028212) with modifications described above.
identifiers.namespace: GEO
identifiers.id: GSM4121481