GSM8972163: ChIPseq_shPHF8_rep2; Mus musculus; ChIP-Seq
For RNA-seq, RNA was extracted using High pure RNA isolation kit from Roche followed by DnaseI treatment. For ChIP-seq, NSCs were cross-linked with Cross-link Gold 0.4% (Diagenode, C01019027) in PBS 30 minutes, and then fixed with methanol-free formaldehyde 1% for 10 min and stopped with 0.125 mM glycine for 10 minutes. Sonication was performed using a Bioruptor sonicator. For ATAC-seq, cells were scrapped and resuspended in RBS buffer and then Igepal CA-630 0.1% was added to achieve cell lysis. Transposition reaction with Transposes enzyme and buffer kits (Illumina, FC-121-1030) and immediately following transposition, DNA was purified. For RNA-seq, libraries were prepared using the TruSeq Stranded Total RNA Sample Preparation kit with Ribo-Zero Human/Mouse/Rat Kit (ref. RS-122-2201/2, Illumina) according to the manufacturer's protocol. Briefly, 500 ng of total RNA was used for ribosomal RNA depletion RNA libraries were prepared for sequencing using standard Illumina protocols (Illumina High HiSeq 2500) For ChIP-seq, the libraries were prepared and amplified to make DNA NanoBall (DNB). Libraries were loaded into a nanoarray and single end 50 base pairs reads were generated by combinatorial Probe-Anchor synthesis (cPAS) For ATAC-seq, Nextera DNA Library Prep Kit (FC-121-1030), along with unique dual index barcodes for each sample and NEBNext High-Fidelity 2x PCR Master Mix (New England Lab, M0541) were used. Ampure XP beads (Beckman Coulter, A63880) were prepared for size selection. Libraries were then pair-end sequenced using NextSeq2000 and approximately 50M reads per sample were obtained.
GEO
GSM8972163_r1