Sequencing data from CUT&RUN were analyzed by CUT-RUNTOOLS-2.064 (link) using default settings (
CUT&RUN Profiling of Chromatin Regulators
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Corresponding Organization : University of Pennsylvania
Other organizations : Children's Hospital of Philadelphia, St. Jude Children's Research Hospital, Pennsylvania State University
Variable analysis
- Cell type used for CUT&RUN: 0.5-1 million undifferentiated HUDEP2, HUDEP2 at day 2 of differentiation, or primary cells at day 8 of differentiation
- Binding of transcription factors NFIA and NFIX, and histone modification H3K27ac, as measured by CUT&RUN
- Experimental procedures followed published protocols from the Henikoff laboratory with minor adaptations
- Antibody incubations were performed in 300 μl PCR tubes for 2 h at 4 °C with rotation
- PAG-MNase were obtained from Cell Signaling
- Approximately 2 μg antibody were used per 200 μl reaction
- The released DNA fragments were quantified by Qubit and sequencing libraries were generated using NEB Kits (E7645 and E6440S) with 15-30 ng input DNA
- The barcoded libraries were pooled and paired-end (2×50 bp) sequenced on the Illumina Nextseq 2000 platform
- Sequencing data from CUT&RUN were analyzed by CUT-RUNTOOLS-2.0 using default settings
- IgG (Cell signaling, #3900)
- Not explicitly mentioned
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