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ERG ERG ERG ERG ERG ZFP367 ZFP367 ZFP367 ZFP367 according ZFP367 We from genes E2F4 E2F4 E2F4 E2F4 E2F4 . are E2F1 E2F1 E2F1 E2F1 E2F1 ZFP960 ZFP960 ZFP960 ZFP960 ZFP960 PHF20 PHF20 PHF20 PHF20 PHF20 compiled SCRT1 SCRT1 SCRT1 SCRT1 SCRT1 MSigDB SP9 SP9 SP9 SP9 SP9 consistent is DPF1 DPF1 DPF1 DPF1 DPF1 KDM5B KDM5B KDM5B KDM5B KDM5B and HIF3A HIF3A HIF3A HIF3A HIF3A 7 HIF1A HIF1A HIF1A HIF1A HIF1A TRN) , C030039L03RIK C030039L03RIK C030039L03RIK C030039L03RIK C030039L03RIK to ANKZF1 ANKZF1 ANKZF1 ANKZF1 ANKZF1 and, PLAGL2 PLAGL2 PLAGL2 PLAGL2 PLAGL2 REL REL REL REL REL gene the Figure S17 . gene NFKB2 NFKB2 NFKB2 NFKB2 NFKB2 For NFKB1 NFKB1 NFKB1 NFKB1 NFKB1 ELF1 ELF1 ELF1 ELF1 ELF1 Figure Figure among DMRT1 DMRT1 DMRT1 DMRT1 DMRT1 for TF CREB1 CREB1 CREB1 CREB1 CREB1 each ATF2 ATF2 ATF2 ATF2 ATF2 sets sets PEG3 PEG3 PEG3 PEG3 PEG3 - the PRRX1 PRRX1 PRRX1 PRRX1 PRRX1 TF HMGA2 HMGA2 HMGA2 HMGA2 HMGA2 ZFP534 ZFP534 ZFP534 ZFP534 ZFP534 HOXB1 HOXB1 HOXB1 HOXB1 HOXB1 RXRA RXRA RXRA RXRA RXRA MYT1L MYT1L MYT1L MYT1L MYT1L S16 0 1 2 3 4 5 6 7 8 9 0 2 4 6 8 10 0 1 2 3 4 5 6 0 1 2 3 4 5 0 1 2 3 4 5 6 7 8 9 10 11.
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    Methods Mice: 4-6 weeks old female C57BL/6 mice obtained from Jackson labs were used for cell isolation. Female Foxp3-IRES-GFP reporter mice (1), backcrossed to B6/C57 background for 10 generations, were used for the isolation of naïve CD4 and naïve CD8 cells for the RNAseq experiments. The mice were housed in pathogen-free animal facility in the La Jolla Institute for Allergy and Immunology and were used according to protocols approved by the Institutional Animal Care and use Committee. Preparation of cells: Subsets of thymocytes were isolated by cell sorting as previously described (2), after cell surface staining using CD4 (GK1.5), CD8 (53-6.7), CD3ε (145- 2C11), CD24 (M1/69) (all from Biolegend). DP cells: CD4+CD8 int/hi; CD4 SP cells: CD4CD3 hi, CD24 int/lo; CD8 SP cells: CD8 int/hi CD4 CD3 hi, CD24 int/lo (Fig S2). Peripheral subsets were isolated after pooling spleen and lymph nodes. T cells were enriched by negative isolation using Dynabeads (Dynabeads untouched mouse T cells, 11413D, Invitrogen). After surface staining for CD4 (GK1.5), CD8 (53-6.7), CD62L (MEL-14), CD25 (PC61) and CD44 (IM7), naïve CD4+CD62L hiCD25-CD44lo and naïve CD8+CD62L hiCD25-CD44lo were obtained by sorting (BD FACS Aria). Additionally, for the RNAseq experiments, CD4 and CD8 naïve cells were isolated by sorting T cells from the Foxp3- IRES-GFP mice: CD4+CD62LhiCD25–CD44lo GFP(FOXP3)– and CD8+CD62LhiCD25– CD44lo GFP(FOXP3)– (antibodies were from Biolegend). In some cases, naïve CD4 cells were cultured in vitro under Th1 or Th2 polarizing conditions (3, 4).
  • Supplemental Materials ZNF281 Enhances Cardiac Reprogramming

    Supplemental Materials ZNF281 Enhances Cardiac Reprogramming

    Supplemental Materials ZNF281 enhances cardiac reprogramming by modulating cardiac and inflammatory gene expression Huanyu Zhou, Maria Gabriela Morales, Hisayuki Hashimoto, Matthew E. Dickson, Kunhua Song, Wenduo Ye, Min S. Kim, Hanspeter Niederstrasser, Zhaoning Wang, Beibei Chen, Bruce A. Posner, Rhonda Bassel-Duby and Eric N. Olson Supplemental Table 1; related to Figure 1. Supplemental Table 2; related to Figure 1. Supplemental Table 3; related to the “quantitative mRNA measurement” in Materials and Methods section. Supplemental Table 4; related to the “ChIP-seq, gene ontology and pathway analysis” and “RNA-seq” and gene ontology analysis” in Materials and Methods section. Supplemental Figure S1; related to Figure 1. Supplemental Figure S2; related to Figure 2. Supplemental Figure S3; related to Figure 3. Supplemental Figure S4; related to Figure 4. Supplemental Figure S5; related to Figure 6. Supplemental Table S1. Genes included in human retroviral ORF cDNA library. Gene Gene Gene Gene Gene Gene Gene Gene Symbol Symbol Symbol Symbol Symbol Symbol Symbol Symbol AATF BMP8A CEBPE CTNNB1 ESR2 GDF3 HOXA5 IL17D ADIPOQ BRPF1 CEBPG CUX1 ESRRA GDF6 HOXA6 IL17F ADNP BRPF3 CERS1 CX3CL1 ETS1 GIN1 HOXA7 IL18 AEBP1 BUD31 CERS2 CXCL10 ETS2 GLIS3 HOXB1 IL19 AFF4 C17ORF77 CERS4 CXCL11 ETV3 GMEB1 HOXB13 IL1A AHR C1QTNF4 CFL2 CXCL12 ETV7 GPBP1 HOXB5 IL1B AIMP1 C21ORF66 CHIA CXCL13 FAM3B GPER HOXB6 IL1F3 ALS2CR8 CBFA2T2 CIR1 CXCL14 FAM3D GPI HOXB7 IL1F5 ALX1 CBFA2T3 CITED1 CXCL16 FASLG GREM1 HOXB9 IL1F6 ARGFX CBFB CITED2 CXCL3 FBLN1 GREM2 HOXC4 IL1F7