Table 1.
Reagents and tools
| Reagent or resource | Source | Identifier |
|---|---|---|
| Antibodies | ||
| Anti‐Sall4 | Santa Cruz | Cat#sc‐166033 |
| Anti‐Sox2 | Stemgent | Cat#09‐0024 |
| Anti‐Oct4 | Santa Cruz | Cat#sc‐5279 |
| Anti‐Nanog | Abcam | Cat#ab80892 |
| Anti‐Tuj1 | BioLegend | Cat#801201 |
| Anti‐ɑ‐SMA | Sigma‐Aldrich | Cat#A2547 |
| Anti‐Foxa2 | Sigma‐Aldrich | Cat#07‐633 |
| Alexa Fluor 488 donkey anti‐mouse lgG (H + L) | Invitrogen | Cat#A21202 |
| Alexa Fluor 555 donkey anti‐mouse lgG (H + L) | Invitrogen | Cat#A31570 |
| Alexa Fluor 555 donkey anti‐rabbit lgG (H + L) | Invitrogen | Cat#A31572 |
| Anti‐IL6 | Invitrogen | Cat#14‐7061‐85 |
| Anti‐Flag | Sigma‐Aldrich | Cat#F1804 |
| Anti‐NFATc4 | Invitrogen | Cat# PA1‐021 |
| Goat anti‐mouse IgG | Kitgen | Cat#GMI06 |
| Bacterial strains | ||
| DH5ɑ | ANGYUBIO | Cat#AYBIO‐G6016 |
| Chemicals, peptides, and recombinant proteins | ||
| R406 | APExBIO | Cat#A5880 |
| FK506 | TargetMol | Cat#T2144 |
| R788 | MCE | Cat#HY‐13038B |
| Lenvatinib | MCE | Cat#HY‐10981 |
| Sunitinib | MCE | Cat#HY‐10255A |
| Crotonic acid | Sigma‐Aldrich | Cat#802650 |
| BrdU | TargetMol | Cat#T6794 |
| Polybrene | Santa Cruz | Cat#sc‐134220 |
| Valproic acid | MCE | Cat#HY‐10585A |
| CHIR99021 | TargetMol | Cat#T2310 |
| 616452 | TargetMol | Cat#T6337 |
| Parnate | TargetMol | Cat#T7942 |
| Forskolin | TargetMol | Cat#T2939 |
| AM580 | MCE | Cat#HY‐10475 |
| EPZ004777 | APExBIO | Cat#A4170 |
| Vitamin C | Sigma‐Aldrich | Cat#A8960 |
| 3‐deazaneplanocin A | APExBIO | Cat#A1905 |
| 5‐aza‐dC | TargetMol | Cat#T1339 |
| SGC0946 | TargetMol | Cat#T3082 |
| PD0325901 | TargetMol | Cat#T6189 |
| Hydroxylamine | Sigma‐Aldrich | Cat#467804 |
| NAC | Sigma‐Aldrich | Cat#A9165 |
| l‐serine (1–13C) | Cambridge Isotope Laboratories | Cat#CLM‐1573‐PK |
| l‐Serine | Sigma‐Aldrich | Cat#S4500 |
| l‐Glycine | Sigma‐Aldrich | Cat#G7126 |
| l‐Threonine | Sigma‐Aldrich | Cat#T8441 |
| Monobromobimane | Sigma‐Aldrich | Cat#B4380 |
| Sulfide dibimane | DOJINDO | Cat#SB15 |
| Recombinant mouse IL‐6 | R&D system | Cat#406‐ML‐005 |
| Mouse LIF | Sigma‐Aldrich | Cat#ESG1107 |
| bFGF | PeproTech | Cat#100‐18B |
| DMEM basic | Gibco | Cat#C11995500CP |
| Penicillin‐Streptomycin | Gibco | Cat#15140‐122 |
| Non‐essential amino acids | Gibco | Cat#11140‐050 |
| 2‐Mercaptoethanol | Sigma‐Aldrich | Cat#M3148 |
| Fetal bovine serum | Gibco | Cat#10270‐106 |
| Knockout serum replacement | Gibco | Cat#10828‐028 |
| Assay kits | ||
| FastPure Cell/Tissue Total RNA Isolation Kit | Vazyme | Cat#RC101‐01 |
| Endo‐Free Plasmid Mini Kit | Omega | Cat#D6950 |
| Agarose Gel DNA Extraction Kit | Easydo | Cat#0103050 |
| BCIP/NBT Alkaline Phosphatase Color Development Kit | Beyotime | Cat#C3206 |
| NovoNGS® CUT&Tag 2.0 High‐Sensitivity Kit (for Illumina®) | Novoprotein | Cat#N259‐YH01 |
| GSH and GSSG Assay Kit | Beyotime | Cat#S0053 |
| BCA Protein Assay Kit | Beyotime | Cat#P0012 |
| Reactive Oxygen Species Assay Kit | Beyotime | Cat#S0033S |
| XFp Cell Mito Stress Test Kit | Agilent Technologies | Cat#103010‐100 |
| Lipid Peroxidation MDA Assay Kit | Beyotime | Cat#S0131S |
| Deposited data | ||
| RNA‐seq data | This paper | GEO: GSE154687 |
| CUT&Tag data | This paper | GEO: GSE154687 |
| Experimental models: Cell & mouse lines | ||
| Mouse: S2/SvPasCrl (129) | Beijing Vital River Laboratory, Animal Technology | Stock#217 |
| Mouse: CBA‐Tg (Pou5f1‐EGFP)2Mnn/J (OG2) | Xiaoyang Zhao Lab, School of Basic Medical Sciences, Southern Medical University, China | NA |
| Mouse: CB17. Cg‐PrkdcscidLystbg‐J/Crl (SCID Beige) | Beijing Vital River Laboratory, Animal Technology | Cat#405 |
| Oligonucleotides | ||
| shRNA: CTR (sense): 5′‐CCGGCCTAAGGTTAAGTCGCCCTCGCTCGAGCGAGGGCGACTTAACCTTAGGTTTTTG‐3′ | This paper | N/A |
| shRNA: CTR (antisense): 5′‐AATTCAAAAACCTAAGGTTAAGTCGCCCTCGCTCGAGCGAGGGCGACTTAACCTTAGG‐3′ | This paper | N/A |
| shRNA: Syk (sense): 5′‐CCGGGGAGAACCTCATCAGGGAATACTCGAGTATTCCCTGATGAGGTTCTCCTTTTTG‐3′ | This paper | N/A |
| shRNA: Syk (antisense): 5′‐AATTCAAAAAGGAGAACCTCATCAGGGAATACTCGAGTATTCCCTGATGAGGTTCTCC‐3′ | This paper | N/A |
| shRNA: Ppp3ca (sense): 5′‐CCGGTGTGATGAACATCAGGCAGCTCGAGCTGCCTGATGTTCATCACATTTTTG‐3′ | This paper | N/A |
| shRNA: Ppp3ca (antisense): 5′‐AATTCAAAAATGTGATGAACATCAGGCAGCTCGAGCTGCCTGATGTTCATCACA‐3′ | This paper | N/A |
| shRNA: Nfatc1 (sense): 5′‐CCGGGGTCAGTGTGACCGAAGATACCTCGAGGTATCTTCGGTCACACTGACCTTTTTG‐3′ | This paper | N/A |
| shRNA: Nfatc1 (antisense): 5′‐AATTCAAAAAGGTCAGTGTGACCGAAGATACCTCGAGGTATCTTCGGTCACACTGACC‐3′ | This paper | N/A |
| shRNA: Gldc (sense): 5′‐CCGGTAGGGTCTTCATTCAAGAGAACTCGAGTTCTCTTGAATGAAGACCCTATTTTTG‐3′ | This paper | N/A |
| shRNA: Gldc (antisense): 5′‐ AATTCAAAAATAGGGTCTTCATTCAAGAGAACTCGAGTTCTCTTGAATGAAGACCCTA‐3′ | This paper | N/A |
| shRNA: Cbs (sense): 5′‐CCGGATCACAGGGATCGCCAGAAAGCTCGAGCTTTCTGGCGATCCCTGTGATTTTTTTG‐3′ | This paper | N/A |
| shRNA: Cbs (antisense): 5′‐AATTCAAAAAAATCACAGGGATCGCCAGAAAGCTCGAGCTTTCTGGCGATCCCTGTGAT‐3′ | This paper | N/A |
| shRNA: Cth (sense): 5′‐CCGGGCCCAGGGATGGTCAGTTTCTCGAGAAACTGACCATCCCTGGGCTTTTTTG‐3′ | This paper | N/A |
| shRNA: Cth (antisense): 5′‐AATTCAAAAAAGCCCAGGGATGGTCAGTTTCTCGAGAAACTGACCATCCCTGGGC‐3′ | This paper | N/A |
| sgRNA: Syk sg‐1 (sense): 5′‐CACCGCGCCAGAGCCGCAATTACCT–3′ | This paper | N/A |
| sgRNA: Syk sg‐1 (antisense): 5′‐AAACAGGTAATTGCGGCTCTGGCG‐3′ | This paper | N/A |
| sgRNA: Syk sg‐2 (sense): 5′‐CACCGACTCCCGGGGGCCGGTTGAA‐3′ | This paper | N/A |
| sgRNA: Syk sg‐2 (antisense): 5′‐AAACTTCAACCGGCCCCCGGGAGT‐3′ | This paper | N/A |
| Primers for RT–qPCR, see Table 2 | This paper | N/A Software and Algorithms |
| Software and algorithms | ||
| GraphPad Prism | GraphPad Software | http://www.graphpad.com |
| SnapGene | https://www.snapgene.com/ | |
| Rstudio | https://rstudio.com/ | |
| Wave | Agilent | https://www.agilent.com/zh‐cn/products/cell‐analysis/software‐download‐for‐wave‐desktop |
| HISAT2 (v2.1.0) | http://ccb.jhu.edu/software/hisat2/manual.shtml | |
| Stringtie (v2.0) | http://ccb.jhu.edu/software/stringtie/ | |
| Bowtie2 (v2.2.5) | http://bowtie‐bio.sourceforge.net/bowtie2/index.shtml | |
| MACS2 (v2.1.2) | https://pypi.org/project/MACS2/ | |