GSM3733680: WT [ATAC-Seq]; Danio rerio; ATAC-seq
We centrifuged the samples at 500g for 10 min at 4°C.  After removing the supernatant, we added 51 μl of cold PBS (one microliter was used for genotyping) and we centrifuged the samples again at 500g for 10 min at 4°C.  The supernatant was removed and 50 μl of cold lysis buffer, prepared as described (Doganli et al., 2016) was added. Cell pellet was resuspended in 50µl PBS and mixed with 25µl TD-Buffer, 2.5µl Tn5 (Illumina Nextera DNA Sample Preparation Kit), 0.5µl 10% NP-40 and 22µl water. Cell/Tn5 mixture was incubated at 37°C for 30min with occasional snap mixing. Transposase treatment was followed by 30min incubation at 50°C together with 500mM EDTA pH8.0 for optimal recovery of digested DNA fragments. For neutralization of EDTA 100µl of 50mM MgCl2 was added followed by purification of the DNA fragments by MinElute PCR Purification Kit (Qiagen). Amplification of Library together with Indexing was performed as described elsewhere (Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. (2013) Jason D Buenrostro, Paul G Giresi, Lisa C Zaba, Howard Y Chang & William J Greenleaf. Nature Methods. doi:10.1038/nmeth.2688). Libraries were mixed in equimolar ratios and sequenced on NextSeq500 platform using V2 chemistry with 2x38bp paired end mode.
GEO Accession
GSM3733680