GSM3383879: AT-PCM1-1; Mus musculus; ATAC-seq
Whole mouse hearts were harvested at P1. Nuclei was isolated using 2.2M sucrose cushion as described in details in the methodes section. MAN-IP was performed for samples PCM1 and Myc to enrich for specific cell-type nuclei and pure nuclei from 2.2M cushion was used as Input sample. We used 2 independent biological replicates per experimental sample for library construction. To generate ATAC-Seq libraries, we followed the improved ATAC-Seq version called Omni-ATAC from Howard Chang lab (Corces et al., 2017). The detailed method is provided by the authors in the Supplementary protocol 1 in their published work. Very briefly, in this study, upon counting the nuclei using Countess II FL (using DAPI light cube) Automated Cell Counter, 50000 nuclei were pelleted in ATAC-Resuspension Buffer (recipe published in the same study) containing 0.1% Tween-20. The supernatant was carefully discarded. Nuclei pellet was incubated with transposase in the transposition mixture following the above-mentioned protocol. Transposed DNA was cleaned with Zymo DNA Clean and Concentrator-5 Kit (#D4014). This was followed by pre-amplification of transposed fragments, qPCR amplification, followed by KAPA library quantification to determine additional cycles for the final PCR amplification (none to very few additional cycles were required upon following the Omni-ATAC protocol). After final amplification, the ATAC-Seq library was cleaned with Zymo DNA Clean and Concentrator-5 Kit (#D4014) and submitted for Tape Station and Qubit analysis. 4nM of each ATAC-Seq library was used for paired-end sequencing on an Illumina NextSeq 500 Mid Output (130 M) flow cell. Image analysis and base calling were performed with Sanger/Illumina 1.9 pipeline.  
GEO
GSM3383879
GEO Accession
GSM3383879