Journal: Molecular cell

Article Title: ATAC-Me captures prolonged DNA methylation of dynamic chromatin accessibility loci during cell fate transitions

doi: 10.1016/j.molcel.2020.01.004

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: ​ REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and Virus Strains T7 Express lysY/I q Competent E. coli New England Biolabs Cat#C3013I Chemicals, Peptides, and Recombinant Proteins RPMI Medium 1640 Gibco Cat#11875093 GlutaMAX™ Supplement Gibco Cat#35050061 Penicillin-Streptomycin (10,000 U/mL) Gibco Cat#15140122 Sodium Pyruvate (100mM) Gibco Cat#11360070 TrypLE™ Express Enzyme (1X), no phenol red Gibco Cat#12604013 Trypan Blue Stain (0.4%) Gibco Cat#15250061 Fetal Bovine Serum Peak Serum Cat#PS-FB1 Dimethyl Sulfoxide Sigma Cat#D8418 L-Ascorbic acid 2-phosphate Sigma Cat#A8960 Phorbol 12-myristate 13-acetate Sigma Cat#P8139 Schneider's Drosophila Medium Gibco Cat#21720001 T4 DNA Polymerase New England Biolabs Cat#M0203S Klenow Fragment (3'→5' exo-) New England Biolabs Cat#M0212S Ampligase® Enzyme and Buffer Lucigen Cat#A3202K NEBNext® High-Fidelity 2X PCR Master Mix New England Biolabs Cat#M0541S KAPA HiFi HotStart Uracil+ ReadyMix (2X) Roche Cat#07959052001 TRIzol™ Reagent Thermo Fisher Scientific Cat#15596018 IGEPAL® CA-630 Sigma Cat#I8896 Trizma® hydrochloride solution Sigma Cat#T2319 Isopropyl-β-D-thiogalactopyranoside (IPTG) (Dioxane-free) Thermo Fisher Scientific Cat#BP1755–1 Chitin Resin New England Biolabs Cat#S6651S Dimethylformamide Thermo Fisher Scientific Cat#D119–1 5-Methylcytosine dNTP Mix Zymo Research Cat#D1030 Critical Commercial Assays EZ DNA Methylation-Lightning Kit Zymo Research Cat#D5030 SMARTer® Stranded Total RNA Sample Prep Kit - HI Mammalian Takara Bio USA Cat#634874 DNA Clean & Concentrator-5 Zymo Research Cat#D4004 MycoAlert™ Mycoplasma Detection Kit (25 Tests) Lonza Cat#LT07–218 Deposited Data ATAC-seq of THP-1 monocytes stimulated with PMA (0hr and 24hr) This study GEO: {"type":"entrez-geo","attrs":{"text":"GSE130096","term_id":"130096"}} GSE130096 ATAC-Me-seq of THP-1 monocytes stimulated with phorbol 12-myristate 13-acetate (0hr, 0.5hr, 1hr, 2hr, 24hr) This study GEO: {"type":"entrez-geo","attrs":{"text":"GSE130096","term_id":"130096"}} GSE130096 RNA-seq of mRNA from THP-1 monocytes stimulated with phorbol 12-myristate 13-acetate (0hr, 0.5hr, 1hr, 2hr, 24hr) This study GEO: {"type":"entrez-geo","attrs":{"text":"GSE130096","term_id":"130096"}} GSE130096 WGBS of THP-1 monocytes stimulated with phorbol 12-myristate 13-acetate (0hr and 24hr) This study GEO: {"type":"entrez-geo","attrs":{"text":"GSE130096","term_id":"130096"}} GSE130096 H3K27Ac ChIP-seq of phorbol 12-myristate 13-acetate stimulated THP-1 monocytes (0hr and 72hr) Phanstiel, D.H., Van Bortle, K., Spacek, D., Hess, G.T., Shamim, M.S., Machol, I., Love, M.I., Aiden, E.L., Bassik, M.C., and Snyder, M.P. (2017) .

Techniques: Recombinant, Staining, Methylation, Sample Prep, Activation Assay, Plasmid Preparation, Sequencing, Software, Methylation Sequencing, Next-Generation Sequencing