KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| H3 | Abcam | Cat#:1791 |
| H3K9ac | Abcam | Cat#:4441 |
| H4 | Abcam | Cat#:7311 |
| H2A | Abcam | Cat#:18255 |
| H2B | Abcam | Cat#:1790 |
| Gcn5 | Cell Signaling | Cat#:3305S |
| GAPDH | Fitzgerald | Cat#:10R-G109a |
| Prm1 | BriarPatch | Cat#:MAb-Hup1N |
| Prm2 | BriarPatch | Cat#:MAb-Hup2B |
| Lectin PNA | Invitrogen | Cat#:L21409 |
| Goat anti-rabbit IgG (H+L) HRP conjugated | Biorad | Cat#:170-6515 |
| Goat anti-mouse IgG (H+L) HRP conjugated | Biorad | Cat#:172-1011 |
| Biological Samples | ||
| Mouse: 129SVE | Taconic | Taconic#:129SVE-M |
| Mouse: Gcn5fl/fl | Lin et. al., 2008b | NA |
| Mouse: Tg(Stra8-icre)1Reb/J | Jackson Labs | Jax#:008208 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| BSA | Affymetrix | Cat#10857 |
| Bouin’s fixative | Sigma | Cat#:HT10132 |
| Benzonase nuclease | Millipore | Cat#:70746 |
| Protease inhibitor cocktail | Roche | Cat#:4693132001 |
| Trichostatin A | Sigma | Cat#:T1952 |
| Pyronin Y | Sigma | Cat#:213519 |
| Collagenase, Type 1A | Sigma | Cat#:C9891 |
| Trypsin | Sigma | Cat#:T9201 |
| MNase | NEB | Cat#:M0247S |
| DNase | Sigma | Cat#:DNEP |
| Nuclei EZ isolsation buffer | Sigma | Cat#:N3408 |
| PMSF | Sigma | P7626 |
| DTT | Sigma | D9779 |
| Critical Commercial Assays | ||
| KAPA Library Quant Kit | KAPA Biosystems | Cat#:KK4835 |
| Ultra II DNA Library prep kit for Illumina | NEB | Cat#:E7645L |
| RNeasy Mini Kit | Qiagen | Cat#:74106 |
| Script-Seq Complete Gold RNA-seq Kit | Illumina | Cat#:SCL24G |
| Nextera XT Kit | Illumina | Cat#:15028212 |
| NextSeqTM 500 High Output Kit (75 cycles) v2 kit | Illumina | Cat#:FC-404-2005 |
| NextSeqTM 500 High Output Kit (150 cycles) v2 kit | Illumina | Cat#:FC-404-2002 |
| Min Elute PCR Purification Kit | Qiagen | Cat#:28006 |
| PCR Purification Kit | Qiagen | Cat#:28106 |
| DNA 1000 Kit | Agilent | Cat#:5067-1504 |
| DNA High Sensitivity Kit | Agilent | Cat#:5067-4626 |
| SuperSignal West Pico Chemiluminescent Substrate | Thermo | Cat#:34080 |
| Deposited Data | ||
| ATAC-seq | GEO | GEO: GSE134561 |
| RNA-seq | GEO | GEO: GSE134561 |
| MNase-seq | GEO | GEO: GSE134561 |
| MNase-seq | Hammoud et al., 2009 | GEO: GSE15594 |
| MNase-seq | Erkek et al., 2013 | GEO: GSE42629 |
| MNase-seq | Samans et al., 2014 | GEO: GSE47843 |
| ChIP-seq | Bryant et al., 2015 | GEO: GSE56526 |
| ATAC-seq/ChIP-seq | Jung et al., 2017 | GEO: GSE79225 |
| RNA-seq | Hammoud et al., 2014 | GEO: GSE49624 |
| MNase-seq | Wu et al., 2016 | GEO: GSE669390 |
| Oligonucleotides | ||
| ATAC-seq indices, see Table S4 | Buenrostro et. al., 2013 | N/A |
| Software and Algorithms | ||
| Gene ontology analysis | Dennis et. al., 2003 | https://david.ncifcrf.gov/summary.jsp |
| STAR v2.5.2a | Dobin et. al., 2013 | https://github.com/alexdobin/STAR |
| SAMtools | Li et. al., 2009 | http://samtools.sourceforge.net/ |
| BEDtools | Quinlan et. al., 2010 | https://bedtools.readthedocs.io/en/latest/ |
| MACS2 | Zhang et. al., 2008 | https://github.com/taoliu/MACS |
| CEAS | Shin et. al., 2009 | http://liulab.dfci.harvard.edu/CEAS/ |
| DANPOS v2.1.3 | Chen et. al., 2013 | https://sites.google.com/site/danposdoc/ |
| RepEnrich v1.0 | Criscione et. al., 2014 | https://github.com/nskvir/RepEnrich |
| EdgeR | Robinson et. al., 2010 | https://bioconductor.org/packages/release/bioc/html/edgeR.html |
| R | R Core Team, 2017 | https://www.r-project.org/ |
| tophat2 v2.0.11 | Kim et. al., 2013 | https://ccb.jhu.edu/software/tophat/index.shtml |
| HTseq v0.6.1p1 | Anders et. al., 2015 | https://htseq.readthedocs.io/en/release_0.11.1/ |
| bowtie v0.12.7 | Langmead et. al., 2009 | http://bowtie-bio.sourceforge.net/index.shtml |
| HOMER | Heinz et. al., 2010 | http://homer.ucsd.edu/homer/ |