Protocol detail

ChIP-seq Protocol for Epigenetic Profiling

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ChIP procedure is described in Supplementary Methods. The libraries were constructed from 3–10 ng of ChIP samples or 50 ng of input samples using NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs), and quantified using GenNext NGS Library Quantification kit (Toyobo). The fragment length of libraries was assessed using 2200 TapeStation (Agilent). Seventy-five base-pair single-read sequencing was performed on an Illumina NextSeq 500. The MM.1S ChIP-seq data for H3K27Ac (GSM894083), H3K27me3 (GSM1252088), MYC (GSM894108), CDK7 (GSM1121098), CDK9 (GSM1085735) and RNAPII (GSM1070127) were downloaded from NCBI (8 (link),65 (link),66 (link)). Detailed ChIP-seq analysis is descrbed in Supplementary Methods. The ChIP-seq data in this study have been deposited in the GEO database under accession number GSE148046.

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Ohguchi H., Park P.M., Wang T., Gryder B.E., Ogiya D., Kurata K., Zhang X., Li D., Pei C., Masuda T., Johansson C., Wimalasena V.K., Kim Y., Hino S., Usuki S., Kawano Y., Samur M.K., Tai Y.T., Munshi N.C., Matsuoka M., Ohtsuki S., Nakao M., Minami T., Lauberth S., Khan J., Oppermann U., Durbin A.D., Anderson K.C., Hideshima T, & Qi J. (2021). Lysine Demethylase 5A Is Required for MYC-Driven Transcription in Multiple Myeloma. Blood Cancer Discovery, 2(4), 370-387.

Publication 2021

NEBNext Ultra II DNA Library Prep Kit for Illumina GenNext NGS Library Quantification kit 2200 TapeStation NextSeq 500

Base pair Cdk9 Chip Chip seq Library Rnapii

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Variable analysis

independent variables

ChIP procedure described in Supplementary Methods
Library construction using NEBNext Ultra II DNA Library Prep Kit for Illumina
Quantification using GenNext NGS Library Quantification kit
Fragment length assessment using 2200 TapeStation
75 base-pair single-read sequencing on an Illumina NextSeq 500

dependent variables

H3K27Ac, H3K27me3, MYC, CDK7, CDK9, and RNAPII ChIP-seq data

control variables

Input samples (50 ng) used for library construction

controls

Positive controls not explicitly mentioned
Negative controls not explicitly mentioned

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