KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| anti-cMyc antibody | R and D Systems | Cat# MABE282, RRID:AB_11204521 |
| anti-SSEA-1 | R and D Systems | Cat# MAB430, RRID:AB_2208782 |
| anti AlexaFluor 555 nm | Molecular Probes | Cat# A-21422, RRID:AB_141822 |
| anti-Oct4 | Abcam | Cat# ab181557, RRID:AB_2687916 |
| anti-CHD4 | Abcam | Cat# ab72418, RRID:AB_1268107 |
| anti-HDAC1 | Abcam | Cat# ab7028, RRID:AB_305705 |
| anti-Lsd1 | Abcam | Cat# ab17721, RRID:AB_443964 |
| anti-HBO1 | Abcam | Cat# ab124993, RRID:AB_11001813 |
| anti-Oct4 | Santa Cruz Biotechnology | Cat# sc-8628, RRID:AB_653551 |
| anti-H3K4me2 | Abcam | Cat# ab32356, RRID:AB_732924 |
| anti- H3K27Ac | Abcam | Cat# ab4729, RRID:AB_2118291 |
| anti-H3K4me1 | Abcam | Cat# ab8895, RRID:AB_306847 |
| anti-H3K27me3 | Abcam | Cat# ab6002, RRID:AB_305237 |
| anti-β Actin | Santa Cruz Biotechnology | Cat# sc-47778 HRP, RRID:AB_2714189 |
| Anti-Rabbit IgG | Jackson ImmunoResearch Labs | Cat# 111–035-003, RRID:AB_2313567 |
| Anti- Mouse IgG | Jackson ImmunoResearch Labs | Cat# 115–035-003, RRID:AB_10015289 |
| Biological Samples | ||
| pCAG-Myc-Oct4 | Addgene | 13460 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| TRIzol | Invitrogen | 15596026 |
| FspEI | NEB | |
| Protein A magnetic beads | Life Technologies | 10002D |
| Protein G magnetic beads | Life Technologies | 10004D |
| RNase | Roche | 11119915001 |
| Proteinase K | Worthington | LS004222 |
| Quick-RNA™ MiniPrep Plus Kit | ZymoReseach | R1057 |
| Verso One-Step RT-qPCR kit | Thermo Scientific | AB-4104A |
| Alkaline phosphatase staining kit | Sigma | AB0300 |
| GST-Lsd1 | Sigma | SRP0122 |
| Oct4 | Abcam | ab134876 |
| Oct4 | Abcam | ab169842 |
| Bulk Histones | Sigma | H9250 |
| EpiTect Fast Bisulfite Conversion Kit | QIAGEN | 59802 |
| Lipofectamine 2000 | Thermofischer | 11668019 |
| Critical Commercial Assays | ||
| Epigenase™ kit | Epigentek | P-0379 |
| Deposited Data | ||
| Raw and analyzed data | This paper | GSE135225 |
| Experimental Models: Cell Lines | ||
| P19 embryonal carcinoma cells | ATCC | CRL-182 |
| F9 embryonal carcinoma cells | ATCC | CRL-1720 |
| E14Tg2A Embryonic stem cells | MMRRC | 015890-UCD |
| Oligonucleotides | ||
| List of primers used | This paper | Table S4 |
| Software and Algorithms | ||
| Trimmomatic v 0.36 | Bolger et al., 2014 | https://github.com/timflutre/trimmomatic |
| Bowtie2 v.2.3.3 | Langmead and Salzberg, 2012 | http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml |
| Cutadapt v 2.2 | Martin, 2011 | https://cutadapt.readthedocs.io/en/stable/installation.html |
| ENSEMBL Mus musculus reference genome version GRCm38.93 | GRCm38.p2 (Genome Reference Consortium Mouse Reference 38), INSDC Assembly GCA_000001635.4, Jan 2012 | ftp://ftp.ensembl.org/pub/release-98/fasta/mus_musculus/dna/ |
| Custom python scripts | https://github.com/natallah/methylRad | |
| Bismark v 0.18.2 | Krueger and Andrews, 2011 | https://www.bioinformatics.babraham.ac.uk/projects/bismark/ |
| BEDToolsv 2.29.0 | Quinlan and Hall, 2010 | https://bedtools.readthedocs.io/en/latest/ |
| Enhancer Atlas v 2.0 | Gao and Qian, 2019 | http://enhanceratlas.org/ |
| TrimGalore v 0.6.4 | Krueger, 2012 | https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ |
| epic2 2019-Jan-03 | Stovner and Sætrom, 2019 | https://bioepic.readthedocs.io/en/latest/ |
| FastQC v. 0.11.7 | Andrews, 2010 | https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ |
| ChIPseeker v 1.22.0 | Yu etal., 2015a. | https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html |
| Ingenuity Pathway Analysis (IPA) | QIAGEN | https://www.qiagenbioinformatics.com/products/ingenuity-pathway-analysis/?gclid=Cj0KCQiAuefvBRDXARIsAFEOQ9GUaRrR3QZy42lJtb5QHvlHsmCrtw5fOeyRo0d2GEgfWxKTIPwd8w8aArVwEALwwcB |