title: GSM2982731: ATAC-sham-7dpi; Mus musculus; ATAC-seq
library_construction_protocol: Total RNA was extracted from the border zone, remote zone, and the LV of sham-operated mice at 3, 7, and 14 dpi using RNAzol according to manufacturer's instructions (Sigma-Aldrich). Prior to cDNA synthesis, total RNA samples were treated with RNase-free DNase I according to manufacturer's instructions (Invitrogen). The cDNA synthesis was carried out on 500 ng DNase-treated RNA using oligo-dT following the Superscript II system protocol (Invitrogen). For ATAC-seq, isolated nuclei were GFP sorted on a SH800 flow cytometer (Sony). Samples were gated in such a way that debris, nuclei clumps, and nuclei with no cardiomyocyte origin were excluded. A total of 50.000 nuclei per sample was collected and successively washed with PBS and used as input for ATAC-seq. Prior to sequencing, a quality check was performed to assure cardiomyocyte-specific open chromatin For RNA-seq libraries, 40 ng DNase-treated total RNA was amplified and converted to cDNA using the Ovation RNA-seq v2 kit (NuGEN). Amplified cDNA was sheared to an average fragment length of 200-400 bp and used with the SOLiD system (Life Technologies) to generate index-tagged sequencing libraries. Library quality and size distribution were determined with TapeStation (Agilent Technologies). Pooled libraries sequenced on a HiSeq 2500 system (Illumina) with 125 bp single-end reads
attributes.tag: GEO Accession
attributes.value: GSM2982731