CUT&Tag for Histone Modifications

CUT&Tag was performed according to the published CUT&Tag protocol [29 (link)] for nuclei (BMDM, PIM, MB, MT, GAS, ADIPO) or cells (ESC). All buffers were supplemented with 5 mM sodium-butyrate (Sigma, 303410) and 1X complete protease inhibitor (Merck, 1187358000). Protein lo-bind tubes (Eppendorf, EP0030108116) were used to reduce sample loss. For GAS samples, incubation volumes were doubled to account for the tissue debris that remained in the nuclear suspensions since this gave better Tapestation QC results. Antibodies against H3K18la (PTM-Bio, PTM-1406), H3K4me3 (Abcam, ab8580), H3K27me3 (Cell Signaling Technology, C36B11), H3K27ac (Abcam, ab4729), and H3K9me3 (Abcam, ab8898) were used in this study. Libraries were indexed using Nextera Indexes, and 150-bp paired-end sequencing was performed on Illumina Novaseq instruments.

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Galle E., Wong C.W., Ghosh A., Desgeorges T., Melrose K., Hinte L.C., Castellano-Castillo D., Engl M., de Sousa J.A., Ruiz-Ojeda F.J., De Bock K., Ruiz J.R, & von Meyenn F. (2022). H3K18 lactylation marks tissue-specific active enhancers. Genome Biology, 23, 207.

Publication 2022

sodium-butyrate Protein lo-bind tubes PTM-1406 ab8580 ab4729 ab8898 Novaseq instruments

Antibodies Buffers Cells H3k4me3 Nuclei Protease inhibitor Protein Sodium butyrate Tissue

Corresponding Organization :

Other organizations : ETH Zurich, Helmholtz Zentrum München, Universidad de Granada

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Variable analysis

independent variables

Antibodies against H3K18la (PTM-Bio, PTM-1406), H3K4me3 (Abcam, ab8580), H3K27me3 (Cell Signaling Technology, C36B11), H3K27ac (Abcam, ab4729), and H3K9me3 (Abcam, ab8898)

dependent variables

Libraries indexed using Nextera Indexes, and 150-bp paired-end sequencing performed on Illumina Novaseq instruments

control variables

All buffers supplemented with 5 mM sodium-butyrate (Sigma, 303410) and 1X complete protease inhibitor (Merck, 1187358000)
Protein lo-bind tubes (Eppendorf, EP0030108116) used to reduce sample loss
For GAS samples, incubation volumes doubled to account for the tissue debris that remained in the nuclear suspensions since this gave better Tapestation QC results

positive controls

Not explicitly mentioned

negative controls

Not explicitly mentioned

Annotations

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