title: GSM3214321: mouse_OPC_ATAC-seq_control; Mus musculus; ATAC-seq
library_construction_protocol: RNA-seq: Total RNA was extracted per the Trizol (Life Technologies) protocol and cleanup using Rneasy kit (Qiagen). Chip-seq: In brief, chromatin was cross-linked and sheared with a Covaris S220 sonicator from primary oligodendrocyte cultures of newborn rat or mouse cortex. Immunoprecipitation was overnight at 4°C using antibodies directed against or control immunoglobulins in the presence of protein A/G Sepharose CL-4B beads (Life Technologies) pretreated with BSA. Rabbit anti-CHD8 (ab114126) antibodies were used for immunoprecipitation. After reverse crosslink, proteinase K treatment, the precipitated chromatin DNA was purified. RNA-seq: RNA-seq libraries from control and mutant OPC cells were prepared using Illumina RNA-Seq Preparation Kit and sequenced using a HiSeq 2500 sequencer. Chip-seq: libraries were prepared using NEBNext ChIP-seq Library Prep Master Mix Set for Illumina (NEB cat # E6240L), and then to sequence on the Illumina sequencer HS2500. ATAC-seq: ATAC-seq assays were performed as previously described (Buenrostro et al., 2013). Briefly, we isolated nuclei of 30,000 sorted cells from the mouse cortex in a cold lysis buffer. Immediately after the nuclei preparation, we performed the transposase reaction for 30 min at 37 °C. The samples were purified using a Qiagen MinElute kit. Following purification, we amplified library fragments using 1× NEBnext PCR master mix.
attributes.tag: GEO Accession
attributes.value: GSM3214321