KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| CK7 | Damsky et al., 1992 | 7D3 |
| H3K4me1 | Millipore | 07-431 |
| H3K4me3 | Cell Signaling | C4208 |
| H3K9ac | Abcam | Ab10812; RRID: AB_297491 |
| H3K9me3 | Abcam | Ab8898; RRID: AB_306848 |
| H3K27me3 | Millipore | CS200603; RRID: AB_2616281 |
| H3K27ac | Abcam | Ab4729; RRID: AB_2118291 |
| Pan-H3 | Abcam | Ab1791; RRID: AB_302613 |
| TRITC | Jackson Immuno Research | 712-025-153; RRID: AB_2340636 |
| FITC | Jackson Immuno Research | 711-095-152; RRID: AB_2315776 |
| HRP | Jackson Immuno Research | 711-035-152; RRID: AB_10015282 |
| H3K27ac | Abcam | Ab4729; RRID: AB_2118291 |
| H3K27ac | Hiroshi Kimura lab | #2 |
| H3K9me3 | Diagenode | pAb-056-050; RRID: AB_2616051 |
| H3K27me3 | Diagenode | pAb-069-050; RRID: AB_2616049 |
| H3K36me3 | Abcam | ab9050; RRID: AB_306966 |
| H3K4me1 | Diagenode | pAb-037-050; RRID: AB_2561054 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Ultra Pure Water | Invitrogen | 10977-023 |
| Anhydrous Ethyl Alcohol | Commercial Alcohols | People Soft ID: 23873 |
| DNA away | Molecular Bioproducts | 7010 |
| 1M Tris solution, pH 8.0 | Ambion | AM9856 |
| Triton X-100, laboratory grade | Sigma | X100-100ML |
| 20% SDS Solution | Ambion | AM9820 |
| 5M NaCl | Ambion | AM9760G |
| 1M DTT | Invitrogen | P2325 |
| 1M Tris HCl pH 7.5 | Invitrogen | 15567-027 |
| 0.5M EDTA | Ambion | AM9260G |
| Deoxycholic Acid, Sodium Salt | Fisher Scientific | AC218590250 |
| Sodium Bicarbonate | Sigma Aldrich | S5761-500G |
| PCR Clean ChIPSeq Beads with 30% PEG | Aline Biosciences | C-1007 |
| Micrococcal Nuclease | NEB | M0247S |
| Dynabeads Protein G | Invitrogen | 100-04D |
| Dynabeads Protein A | Invitrogen | 100-02D |
| Protease Inhibitor Cocktail | Calbiochem | 539134 |
| Buffer G2 | Qiagen | 1014636 |
| Qiagen Protease | Qiagen | 19155 |
| EB buffer | Qiagen | 19570 |
| Sodium Butyrate | Millipore | 19-137 |
| Deposited Data | ||
| Infinium 450k data | This paper | GEO: GSE98938 |
| Bisulfite-seq, ChIP-seq, and RNA-seq data from Roadmap Epigenomics Program UCSF | This paper | ENA: SRP046944 |
| ChIP-seq and RNA-seq data | This paper | EGAD00001006066 |
| Codes, original/unprocessed, and processed data | This paper | https://github.com/Zhang-lab/Placenta_Epigenome |
| The browser containing all sequencing data tracks in an easily accessible format | This paper | https://urldefense.proofpoint.com/v2/url?u=https-3A__epigenomegateway.wustl.edu_browser_-3Fgenome-3Dhg19-26hub-3Dhttps-3A__remc.wustl.edu_dli_placenta-5Fhub_hub&d=DwIGaQ&c=iORugZls2LlYyCAZRB3XLg&r=5wrWvGv7RP_8tjyr12sx9_Bl0J4jdg2EScdfn8GA158&m=VWXeapLJmLvKGAMDKKXPlmo0t5yoFgMVBGpslGkfUf0&s=VElNqkL_fzdXrZSw4AjnGgGXzCx7XDo1EtOO12o2ark&e= |
| Software and Algorithms | ||
| Bismark (v. 0.16.1) | Krueger et al., 2011 | https://www.bioinformatics.babraham.ac.uk/projects/bismark/ |
| Bowtie (v. 1.1.0) | Langmead et al., 2009 | http://bowtie-bio.sourceforge.net/index.shtml |
| Bismark Methylation Extractor | Krueger et al., 2011 | https://www.bioinformatics.babraham.ac.uk/projects/bismark/ |
| STAR version 2.4.2a81 | Dobin et al., 2013 | https://github.com/alexdobin/STAR |
| featureCounts, version 1.4.6 | SuBread | http://subread.sourceforge.net/ |
| R/Bioconductor package edgeR | Robinson et al., 2010 | https://bioconductor.org/packages/release/bioc/html/edgeR.html |
| BWA (0.6.2-4126 or 0.7.6a-sb) | Durbin et al., 2010 | http://bio-bwa.sourceforge.net/ |
| Samtools | Li et al., 2009 | http://samtools.sourceforge.net/ |
| Sambamba (0.7.1) | Tarasov et al., 2015 | https://lomereiter.github.io/sambamba/ |
| MethylQA (0.1.5) | Li et al., 2015 | http://methylqa.sourceforge.net/ |
| MACS2 (2.0.10 or 2.1.1.20160309) | Zhang et al., 2008 | https://github.com/macs3-project/MACS |
| bedtools (v2.25.0) | Quinlan et al., 2010 | https://bedtools.readthedocs.io/en/latest/content/overview.html |
| deepTools (3.4.2) | Ramirez et al., 2014 | https://deeptools.readthedocs.io/en/develop/ |
| GREAT (3.0.0) | McLean et al., 2010 | http://great.stanford.edu/public/html/ |
| MSigDB (GSEA website; v7.0) | Liberzon et al., 2011 | https://www.gsea-msigdb.org/gsea/msigdb |
| DAVID (6.8) | Sherman et al., 2007 | https://david.ncifcrf.gov/ |
| HOMER | UCSD | http://homer.ucsd.edu/homer/motif/ |
| ImageJ | NIH | https://imagej.nih.gov/ij/ |
| Other | ||