KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Rabbit polyclonal anti-SHMT2 | Abcam | Cat# ab224428; RRID:AB_2861139 |
| Rabbit monoclonal anti-BTG4 | Abcam | Cat# ab206914; RRID:AB_2861140 |
| Sheep polyclonal anti-BubR1 | Abcam | Cat# ab28193; RRID:AB_444307 |
| Mouse monoclonal anti-Myc | Abcam | Cat# ab18185; RRID:AB_444307 |
| Rabbit polyclonal anti-H3K4me3 | Abcam | Cat# ab8580; RRID:AB_306649 |
| Human anti-Centromere CREST | Fitzgerald Industries International | Cat# 09C-CS1058; |
| Rabbit polyclonal anti-NKAP | GeneTex | Cat# GTX120929; RRID:AB_2861141 |
| Mouse monoclonal anti-β-actin | Sigma | Cat# A5441; RRID:AB_476744 |
| Mouse monoclonal anti-GAPDH | Proteintech | Cat# HRP-60004; RRID:AB_2737588 |
| Mouse monoclonal anti-α-tubulin-FITC | Sigma | Cat# F2168; RRID:AB_476967 |
| Goat anti-rabbit IgG-FITC | Thermo Fisher | Cat# 65–6111; RRID:AB_2533966 |
| Goat anti-rabbit IgG-HRP | Thermo Fisher | Cat# 81–1620, RRID:AB_2534006 |
| Bacterial and Virus Strains | ||
| TOP10 Competent E. coli | TIANGEN | Cat# CB104 |
| Biological Samples | ||
| Oocyte | This Study | N/A |
| Sperm | This Study | N/A |
| Embryo | This Study | N/A |
| Chemicals, Peptides, and Recombinant Proteins | ||
| 3’-AMP | Sigma-Aldrich | Cat# A9272 |
| 3-Methylxanthine | Adamas | Cat# 13392B |
| 5’-Methylthioadenosine | Sigma-Aldrich | Cat# D5011 |
| Adenine | Aladdin | Cat# A108804 |
| Adenosine | Adamas | Cat# 67712A |
| Arachidonic acid | Sigma-Aldrich | Cat# A3611 |
| Beta-Alanine | Sigma-Aldrich | Cat# 146064 |
| Cholesterol | Aladdin | Cat# C104029 |
| Cholic acid | Adamas | Cat# 84576A |
| cis-Aconitic acid | Aladdin | Cat# A111230 |
| Citric acid | Aladdin | Cat# C108872 |
| Cytidine | Adamas | Cat# 74476A |
| Deoxycytidine | Sigma-Aldrich | Cat# D3897 |
| D-Glucuronic acid | Sigma-Aldrich | Cat# G5269 |
| D-Glucurono-6,3-lactone | Adamas | Cat# 48251A |
| D-Glutamic acid | Sigma-Aldrich | Cat# V900450 |
| Dihydrotestosterone | Dr.E | Cat# DRE-C10255010 |
| Docosahexaenoic acid | Sigma-Aldrich | Cat# D2534 |
| Dodecanoic acid | Adamas | Cat# 23651A |
| Eicosapentaenoic acid | Aladdin | Cat# E100927 |
| Fumaric acid | Adamas | Cat#14061B |
| Gluconolactone | Adamas | Cat# 89621A |
| Glucose 6-phosphate | TRC | Cat# G595338 |
| Glyceraldehyde | Sigma-Aldrich | Cat# G5001 |
| Glycine | Adamas | Cat# 65953A |
| Glycocholic acid hydrate | Sigma-Aldrich | Cat# G2878 |
| Hypotaurine | Sigma-Aldrich | Cat# H1384 |
| Inosine | Adamas | Cat# 67731A |
| Inosinic acid | Sigma-Aldrich | Cat# I2879 |
| L-Aspartyl-L-phenylalanine | Sigma-Aldrich | Cat# 421669 |
| L-Carnitine | Adamas | Cat# 64024A |
| L-Cystine | Aladdin | Cat# C108225 |
| L-Dihydroorotic acid | Sigma-Aldrich | Cat# D7128 |
| Levulinic acid | Adamas | Cat# 18284A |
| L-Histidine | Aladdin | Cat# H108260 |
| L-Leucine | Adamas | Cat# 70880A |
| L-Palmitoylcarnitine chloride | Sigma-Aldrich | Cat# P4509 |
| L-Serine | Adamas | Cat# 65987B |
| L-Tryptophan | Adamas | Cat# 79767B |
| Myristic acid | Adamas | Cat# 64434B |
| N-Acetyl-L-methionine | Adamas | Cat# 74718A |
| N-Acetylneuraminic acid | Aladdin | Cat# A100555 |
| Niacinamide | Adamas | Cat# 92273A |
| Norvaline | Sigma-Aldrich | Cat# N7627 |
| Octadecanamide | Sigma-Aldrich | Cat# O601 |
| Oxidized glutathione | Aladdin | Cat# G105428 |
| Pantothenol | Sigma-Aldrich | Cat# 76200 |
| Putrescine | Aladdin | Cat# D110948 |
| Pyridoxal 5’-phosphate hydrate | Sigma-Aldrich | Cat# P9255 |
| Pyroglutamic acid | Adamas | Cat# 92246A |
| Retinal | Sigma-Aldrich | Cat# R2500 |
| S-adenosylmethionine | Sigma-Aldrich | Cat# A2408 |
| Sorbitol | Adamas | Cat# 60805A |
| Spermine | Aladdin | Cat# S109704 |
| Taurocholic Acid sodium salt hydrate | Sigma-Aldrich | Cat# T4009 |
| Uridine | Aladdin | Cat# U108810 |
| Xanthosine dihydrate | Sigma-Aldrich | Cat# X0750 |
| (−)-Matairesinol | Supelco | Cat# 04157 |
| 1-Palmitoyl-Palmitoyl | Sigma-Aldrich | Cat# L5254 |
| 2-Furoic acid | Adamas | Cat# 87865A |
| 2-Hydroxypalmitic Acid | Sigma-Aldrich | Cat# H7021 |
| 3,4,5-Trimethoxycinnamic acid | Adamas | Cat# 89485A |
| 3-Phenylbutyric Acid | Sigma-Aldrich | Cat# 116807 |
| 4-Methylcatechol | Adamas | Cat# 58208B |
| 5-Aminolevulinic acid hydrochloride | Sigma-Aldrich | Cat# A3785 |
| 5-Hydroxylysine hydrochloride | Sigma-Aldrich | Cat# H0377 |
| 5-Hydroxymethyl-2-Deoxyuridine | Sigma-Aldrich | Cat# H8631 |
| Agmatine Sulfate | Sigma-Aldrich | Cat# A7127 |
| Allantoin | Adamas | Cat# 91922A |
| Aminocaproic acid | Adamas | Cat# 69197A |
| Argininosuccinic acid | Sigma-Aldrich | Cat# 73097 |
| Biotin | Adamas | Cat# 67896A |
| Capric acid | Adamas | Cat# 49153A |
| Cortisol | Adamas | Cat# 60344A |
| Cortisone | Aladdin | Cat# C119445 |
| Cyclic AMP | Adamas | Cat# 69704A |
| Cytosine | Adamas | Cat# 78600A |
| Dehydroepiandrosterone | Supelco | Cat# D-063 |
| Deoxycholic acid | Adamas | Cat# 85460B |
| Deoxycholic acid glycine conjugate | Aladdin | Cat# G113438 |
| D-Glucaric acid potassium salt | Sigma-Aldrich | Cat# S4140 |
| Dihydroxyacetone phosphate | Sigma-Aldrich | Cat# 51269 |
| Dodecanedioic acid | Adamas | Cat# 77196A |
| Estriol | Adamas | Cat# 60385A |
| Estrone | Adamas | Cat# 63010A |
| Glycerophosphocholine | Adamas | Cat# 44657A |
| Glycolic acid | Adamas | Cat# 83663A |
| Guanine | Aladdin | Cat# G104274 |
| Hexadecanedioic acid | Adamas | Cat# 60631A |
| Histamine dihydrochloride | Sigma-Aldrich | Cat# 53300 |
| Hyodeoxycholic acid | Aladdin | Cat# H106315 |
| Isocitric acid trisodium salt hydrate | Sigma-Aldrich | Cat# I1252 |
| L-3-Phenyllactic acid | Adamas | Cat# 35411B |
| L-Cysteine | Adamas | Cat# 62776B |
| L-Dopa | Adamas | Cat# 68867A |
| L-Lysine | Adamas | Cat# 66313B |
| L-Malic acid | Adamas | Cat# 91942A |
| L-Phenylalanine | Adamas | Cat# 73340B |
| Melatonin | Adamas | Cat# 79824B |
| N-Acetylethylenediamine | Sigma-Aldrich | Cat# 397261 |
| N-Acetylglutamic acid | Adamas | Cat# 16378A |
| N-Alpha-acetyllysine | Sigma-Aldrich | Cat# A2010 |
| Neopterin | Sigma-Aldrich | Cat# N3386 |
| N-Formyl-L-methionine | Sigma-Aldrich | Cat# F3377 |
| Orotic acid | Adamas | Cat# 74736A |
| Pentadecanoic acid | Supelco | Cat# 91446 |
| Petroselinic acid | Sigma-Aldrich | Cat# P8750 |
| Prostaglandin E2 | Sigma-Aldrich | Cat# P5640 |
| Prostaglandin F2a | TCI | Cat# P1885 |
| Quinic acid | Sigma-Aldrich | Cat# 138622 |
| Rhamnose | Adamas | Cat# 51662A |
| Riboflavin | Adamas | Cat# 85641A |
| Succinic acid | Adamas | Cat# 14056B |
| Syringic acid | Adamas | Cat# 62915A |
| Taurine | Adamas | Cat# 13304A |
| Testosterone | Aladdin | Cat# T102169 |
| Tetradecanedioic acid | Sigma-Aldrich | Cat# D221201 |
| Thyroxine | Aladdin | Cat# T106193 |
| Trizma Acetate | Sigma-Aldrich | Cat# V900448 |
| Tryptophanol | Sigma-Aldrich | Cat# 469971 |
| Xanthurenic acid | Sigma-Aldrich | Cat# D120804 |
| M16 medium | Sigma-Aldrich | Cat# M7292 |
| HTF medium | Merck Millipore | Cat# MR-070 |
| KSOM medium | Merck Millipore | Cat# MR-106-D |
| Milrinone | Sigma-Aldrich | Cat# M4659 |
| Bovine serum albumin | Sigma-Aldrich | Cat# A1470 |
| Mineral oil | Sigma-Aldrich | Cat# M8410 |
| INDO | Selleck Chemicals | Cat# S5010 |
| Sesamin | Selleck Chemicals | Cat# S2392 |
| Curcumin | Selleck Chemicals | Cat# S1848 |
| BWA4C | Sigma-Aldrich | Cat# B7559 |
| propidium iodide | Thermo Fisher | Cat# P3566 |
| Hoechst 33342 | Thermo Fisher | Cat# H3570 |
| Anti-fade medium | Vectashield | Cat# H1000 |
| CM-H2DCFDA | Thermo Fisher | Cat# C6827 |
| Proteinase K | Thermo Fisher | Cat# EO0492 |
| T4 RNA Ligase | Thermo Fisher | Cat# AM2141 |
| AscI endonuclease | New England Biolabs | Cat# R0558S |
| FseI endonuclease | New England Biolabs | Cat# R0588S |
| T4 DNA ligase | New England Biolabs | Cat# M0202S |
| NotI endonuclease | New England Biolabs | Cat# R0189S |
| DpnI endonuclease | New England Biolabs | Cat# R0176S |
| Phusion high-fidelity DNA polymerase | New England Biolabs | Cat# M0530L |
| Critical Commercial Assays | ||
| Arcturus PicoPure RNA Isolation Kit | Thermo Fisher | Cat# KIT0204 |
| Quantitect Reverse Transcription Kit | Qiagen | Cat# 205311 |
| QIAquick PCR Purification Kit | Qiagen | Cat# 28104 |
| SP6 mMESSAGE mMACHINE Kit | Thermo Fisher | Cat# AM1340 |
| Pierce ECL Western Blotting Substrate | Thermo Fisher | Cat# 32106 |
| SuperScript™ III First-Strand Synthesis SuperMix | Thermo Fisher | Cat# 18080–400 |
| TMTsixplex™ Isobaric Label Reagent Set | Thermo Fisher | Cat# 90066 |
| EZ DNA Methylation-Gold Kit | Zymo Research | Cat# D5005 |
| Deposited Data | ||
| Oocytes proteomics data I | This Study | Project accession: PXD018777; username: reviewer55684@ebi.ac.uk; password: mYMGRG0w. |
| Oocytes proteomics data II | This Study | Project accession: PXD018753; username: reviewer43455@ebi.ac.uk; password: Uz92GHI2. |
| Oocyte metabolomics data | This Study | See Table S1 |
| Oocyte Bisulfite-seq data. | This Study | GEO: GSE149053 |
| Original/source data | This Study | https://data.mendeley.com/datasets/8tftw77m4z/draft?a=f27e269e-9b60–43f2–9ccb-09c720c7a3bb |
| Experimental Models: Cell Lines | ||
| N/A | N/A | N/A |
| Experimental Models: Organisms/Strains | ||
| C57BL/6 mice | Charles River Laboratories | N/A |
| Oligonucleotides | ||
| siRNA sequences for knockdown experiments | This Study | see Table S4 |
| Primer sequences for overexpression analysis | This Study | see Table S4 |
| Primer sequences for Poly(A) tail assay | This Study | see Table S4 |
| Primer sequences for qRT-PCR | This Study | see Table S4 |
| Recombinant DNA | ||
| Plasmid: Myc tags in pCS2+ | This Study | N/A |
| Plasmid: Myc tags-Nkap in pCS2+ | This Study | N/A |
| Plasmid: Myc tags-Nkap mutation in pCS2+ | This Study | N/A |
| Plasmid: Myc tags-Shmt2 mutation in pCS2+ | This Study | N/A |
| Plasmid: Myc tags-G6pdx in pCS2+ | This Study | N/A |
| Software and Algorithms | ||
| ImageJ | NIH | https://imagej.nih.gov/ij/ |
| Prism (V7.0) | GraphPad | https://www.graphpad.com/scientific-software/prism/ |
| R (V2.15.0) | (Davey et al., 1997) | http://cran.r-project.org/ |
| ZEN | ZEISS | https://www.zeiss.com/microscopy/int/downloads.html |
| TraceFinder (V3.1) | Thermo Fisher | https://www.thermofisher.com/us/en/home/industrial/mass-spectrometry/liquid-chromatography-mass-spectrometry-lc-ms/lc-ms-software/lc-ms-data-acquisition-software/tracefinder-software.html |
| SIMCA-P (V14.0) | Umetrics | https://umetrics.com/products/simca |
| KEGG Mapper (V4.1) | Kanehisa et al., 2020 | https://www.genome.jp/kegg/mapper.html |
| MaxQuant (V1.2.2.5) | Cox and Mann, 2008 | https://maxquant.net/maxquant/ |
| DAVID | Huang et al., 2009 | https://david.ncifcrssf.gov/ |
| Perseus software platform (V1.6.2.3) | Tyanova et al., 2016 | https://maxquant.net/perseus/ |
| Pathway Studio (V 6.00) | Nikitin et al., 2003 | https://www.pathwaystudio.com/ |
| Cytoscape (V3.7.2) | Shannon et al., 2003 | https://cytoscape.org/ |
| Trim galore | https://github.com/FelixKrueger/TrimGalore | https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ |
| Bismark | Krueger et al., 2011 | https://www.bioinformatics.babraham.ac.uk/projects/bismark/ |
| Metilene | Jühling et al., 2015 | https://www.bioinf.uni-leipzig.de/Software/metilene/ |
| IGV | Robinson et al., 2011 | https://igv.org/ |
| UCSC Genome Browser | University of California Santa Cruz | http://genome.ucsc.edu/ |
| BEDOPS | Neph et al., 2012 | https://bedops.readthedocs.io/en/latest/index.html |
| Other | ||
| N/A | N/A | N/A |