| Antibodies |
| Mouse monoclonal ANTI-FLAG M2 antibody |
Sigma-Aldrich |
Cat# F1804 |
| Rabbit Anti-Mouse IgG H&L |
abcam |
Cat# ab46540 |
| Guinea Pig Anti-Rabbit IgG (Heavy & Light Chain) |
Antibodies-Online |
Cat# ABIN101961 |
| Anti-Histone H2A.Z antibody, Rabbit polyclonal |
abcam |
Cat# ab4626 |
| Rabbit polyclonal Histone H2B antibody |
Active Motif |
Cat# 39237 |
| Rabbit polyclonal Anti-acetyl-Histone H4 antibody |
Millipore Sigma |
Cat# Upstate 06–598 |
| Rabbit polyclonal Histone H3K4me3 antibody |
Active Motif |
Cat# 39159/60 |
| Mouse monoclonal Histone H3K36me3 antibody |
Active Motif |
Cat# 61021 |
| Chemicals, Peptides, and Recombinant Proteins |
| Protein A-MNase fusion protein |
Henikoff Lab (in-house) |
N/A |
| BioMag Plus Concanavalin A beads |
Bangs Laboratories |
Cat# BP531 |
| Spermidine Trihydrochloride |
Sigma-Aldrich |
Cat# S2501–5G |
| Digitonin |
EMD-Millipore |
Cat# 300410 |
| Roche complete protease inhibitor tablet |
Sigma-Aldrich |
Cat# 11836170001 |
| Proteinase K |
Thermo Fisher Scientific |
Cat# 25530049 |
| RNase A |
Thermo Fisher Scientific |
Cat# EN0531 |
| Glycogen |
Sigma-Aldrich |
Cat# 10901393001 |
| Dynabeads Protein G |
Thermo Fisher Scientific |
Cat# 10004D |
| Dynabeads Protein A |
Thermo Fisher Scientific |
Cat# 10002D |
|
Drosophila mononucleosomal DNA |
Henikoff Lab (in-house) |
N/A |
|
S. pombe mononucleosomal DNA |
Henikoff Lab (in-house) |
N/A |
| Ampure XP beads |
Beckman Coulter |
Cat# A29153 |
| Deposited Data |
| All sequencing datasets have been uploaded in GEO under accession GEO: GSE116853
|
This paper |
GEO: GSE116853
|
| H3Q85C chemical cleavage mapping |
(Chereji et al., 2018) |
GEO: GSE97290
|
| RSC CUT&RUN |
(Skene and Henikoff,2017) |
GEO: GSE84474
|
| H2A.Z, H3K4me3 and H3K36me3 ChIP-seq |
(Weiner et al., 2015) |
GEO: GSE61888
|
| NET-seq |
(Churchman and Weissman, 2011) |
GEO: GSE25107
|
| Experimental Models: Organisms/Strains |
|
S. cerevisiae: W1588–4C sth1–3FLAG-kanMX4 |
Laboratory of Toshi Tsukyama |
YTT3249 |
|
S. cerevisiae: W1588–4C htz1–2L-3FLAG-kanMX4 |
Laboratory of Toshi Tsukyama |
YTT1724 |
|
S. cerevisiae: htb1–3FLAG |
Laboratory of Sue Biggins |
SBY4554 |
|
S. cerevisiae: W1588–4C abf1–3FLAG- kanMX |
Henikoff Lab |
(Kasinathan et al., 2014) |
|
S. cerevisiae: W1588–4C reb1–3FLAG- kanMX |
Henikoff Lab |
(Kasinathan et al., 2014) |
| Software and Algorithms |
| bedtools |
http://bedtools.readthedocs.io/en/latest/index.html |
v2.27.0 |
| Bowtie2 |
http://bowtie-bio.sourceforge.net/bowtie2/index.shtml |
v2.2.5 |
| Integrated genome browser |
https://wiki.transvar.org/display/igbman/Home |
v9.0.1 |
| gnuplot |
http://gnuplot.info/ |
v3.13.0 |
| Java Tree View |
http://jtreeview.sourceforge.net/ |
v1.1.6r2 |
| Custom shell scripts |
This paper |
N/A |
| Custom perl scripts |
This paper |
N/A |
