CUT&RUN: Profiling Transcription Factor and Histone Modifications

CUT&RUN was performed with the CUTANA ChIC/CUT&RUN Kit (Epicypher, 14-1048). A total of 500,000 cells for each condition were fixed with 1% formaldehyde for 1 min, and the protocol for fixed cells was followed as described in the manual. Antibodies used were rabbit IgG (Epicypher, 13-0042), rabbit anti-YY1 (Cell Signaling Technology, 46395S) at 1:50, and rabbit H3K27ac (ActiveMotif, 39034) at 1:50. Libraries were prepared using the CUTANA ChIC/CUT&RUN Library Prep Kit (Epicypher, 14-1001). Samples were run on the Illumina NextSeq 1000 P2 flow cell, with 50-bp paired end reads. Sequenced reads were analyzed using the nf-core/cutandrun pipeline (20 (link), 21 (link)). Peak calling was performed using SEACR (22 (link)).

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Dai J., SoRelle E.D., Heckenberg E., Song L., Cable J.M., Crawford G.E, & Luftig M.A. (2023). Epstein-Barr virus induces germinal center light zone chromatin architecture and promotes survival through enhancer looping at the BCL2A1 locus. mBio, 15(1), e02444-23.

Publication 2023

CUTANA ChIC/CUT&RUN Kit rabbit anti-YY1 rabbit H3K27ac

Corresponding Organization :

Other organizations : Duke University, Duke Medical Center

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Variable analysis

independent variables

Antibody type (rabbit IgG, rabbit anti-YY1, rabbit H3K27ac)

dependent variables

Sequenced reads
Identified peaks

control variables

Cell number (500,000 cells for each condition)
Fixation (1% formaldehyde for 1 min)
Library preparation (CUTANA ChIC/CUT&RUN Library Prep Kit)
Sequencing (Illumina NextSeq 1000 P2 flow cell, 50-bp paired end reads)
Data analysis (nf-core/cutandrun pipeline, SEACR peak calling)

positive controls

None specified

negative controls

Rabbit IgG

Annotations

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