GSM6765154: R1mESC_FLAG_SP1_CUTaRUN_0000nM; Mus musculus; OTHER
Isolated nuclei of MCF-7, R1 mESC, NPC or F121 cells were incubated with a titration series of FLAG-tagged transcription factor of interest, which was followed up by either ChIP-seq or CUT&RUN with anti-FLAG antibody, including heterologous spike-in DNA (dm6 or S.cerevisiae for ChIP-seq or CUT&RUN-based follow-up, resp.). Released DNA fragments were column purified and used for preparation of sequencing libraries. Libraries were prepared using the Kapa Hyper Prep Kit (Kapa Biosystems) according to manufacturer's protocol, with the following modifications. All input material was used to prepare libraries and 2.5 μl of the NEXTflex adapter stock (600nM, Bioo Scientific) was used for adapter ligation of each sample. Libraries were amplified with 12 PCR cycles and a double post-amplification clean-up was used to ensure proper removal of adapters. Samples were analyzed for purity using a High Sensitivity DNA Chip on a Bioanalyzer 2100 system (Agilent). Libraries were paired-end sequenced on a Illumina NextSeq500.