Total RNA was isolated from HL1 and AC16 cells using RNeasy Mini kit (Qiagen) following the manufacturer's instructions that included the on-column DNase treatment using the RNase-Free DNase set (Qiagen).  RNA quality was assessed using the Bioanalyzer RNA kit (Agilent Technologies) prior to sequencing library preparation. Nuclei were isolated from HL1 and AC16 cells following the lysis protocol by Buenrostro et al. (Nat Methods. 2013;10(12):1213-1218). Illumina TruSeq RNA Sample Preparation Kit v2 (Illumina) was used to generate indexed sequencing libraries following the manufacturer's protocols.  A sample from each library was used to assess library fragment size distribution by electrophoresis, using BioAnalyzer High Sensitivity DNA Assay (Agilent Technologies), and to assess library concentration by qPCR, using the KAPA library quantification kit (KAPA Biosystems).  Equimolar amounts of libraries were pooled and sequenced on an Illumina HiSeq 2500 instrument using standard protocols for paired end 100bp reads with a desired sequencing depth of ~75 million paired end reads per library.  RNA-seq for both cell lines were performed in technical duplicates. ATAC-seq was performed on fresh unfixed HL1 and AC16 cells (~50,000 cells each) following the published protocol (Buenrostro et al. Nat Methods. 2013;10(12):1213-1218).  A sample from each indexed library was used to assess library fragment size distribution by 2% agarose TAE gel electrophoresis and to assess library concentration by qPCR using the KAPA library quantification kit (KAPA Biosystems).  Equimolar amounts of libraries were pooled and sequenced on an Illumina HiSeq 2500 instrument using standard protocols for paired end 50bp sequencing with a desired sequencing depth of ~150 million paired end reads per library.
GEO Accession
GSM2949330