title: GSM3756607: wt_high_atac_rep2; Danio rerio; ATAC-seq
library_construction_protocol: The ATAC-seq protocol (Buenrostro et al., 2014) was performed on approximately 70,000 cells. Zebrafish embryos were first deyolked using buffers as described in (Link et al. 2006); briefly, embryos were dissociated in deyolking buffer by brief vortexing and shaking at 1100 rpm at 4°C. Cells were collected by centrifugation at 400 rcf and the supernatant was removed. Cells were washed two more times with deyolking wash buffer. For the 256-cell stage samples, 300 embryos were manually deyolked. Following dissociation, cells were lysed in cell lysis buffer (Buenrostro et al. 2014). Nuclei were spun down at 500 rcf for 10 minutes at 4°C, resuspended in tagmentation mix and incubated at 37°C for 30 minutes with gentle shaking at 800 rpm. Tagmented DNA was cleaned up using the Qiagen Minelute Reaction Cleanup kit. to make DNA libraries, the number of PCR cycles were determined by qPCR as described in (Buenrostro et al. 2014). Following 11-13 cycles of PCR, the libraries were purified using the Minelute Reaction cleanup kit (Qiagen) and measured with a fragment analyzer. Samples were sequenced following adaptor cleanup
attributes.tag: GEO Accession
attributes.value: GSM3756607