Background
Results
U937 cells were differentiated into monocyte and macrophage-like cells
Differential gene expression of U937 cells manifests functional macrophage phenotype
Illumina array fold change | |||||||
---|---|---|---|---|---|---|---|
Ref.Seq. | Gene Symbol | PMA6 | PMA12 | PMA24 | PMA32 | LPS | VitD3 |
NM_014220 | HL6 | 20.6 | 88.5 | 96.3 | 96.5 | 128.2 | 1.1 |
NM_005368 | MB | 4.3 | 27.8 | 90.5 | 110.5 | 96.2 | 7.7 |
NM_000582 | BNSP | 7.6 | 31.1 | 84.1 | 118.1 | 110.9 | 1 |
NM_021796 | PLAC1 | 1.8 | 11.8 | 34.6 | 39.1 | 34.3 | -1.1 |
NM_002423 | MMP7 | 1.9 | 2.7 | 29.9 | 61.4 | 36.5 | -1.4 |
NM_002922 | RGS1 | 15.9 | 25.6 | 28.6 | 26 | 29.9 | -1.1 |
NM_018993 | RIN2 | 9.5 | 18.2 | 23.2 | 18.9 | 14.4 | 1 |
NM_001955 | EDN1 | 42.9 | 22.9 | 21.2 | 22.9 | 85.4 | 1 |
NM_000265 | NCF1 | 3.4 | 11.2 | 18.6 | 21 | 17.8 | 3.8 |
NM_001332 | CTNND2 | 1.5 | 4.9 | 15.7 | 20.4 | 12.8 | 1.1 |
NM_016270 | KLF2 | 15.5 | 11.6 | 13.9 | 15.2 | 9.8 | -1.3 |
NM_002167 | ID3 | 1.8 | 3.4 | 11.9 | 6.2 | 38.9 | 2.7 |
NM_002203 | CD49B | 2 | 7 | 10.5 | 9.3 | 6.9 | 1 |
NM_000014 | A2M | 4.1 | 7.4 | 10.4 | 11.1 | 11.5 | 1.1 |
NM_001401 | EDG2 | 4.4 | 9.2 | 10.3 | 8.8 | 6.6 | -1.8 |
NM_152591 | CCDC63 | 2.5 | 7.1 | 9.9 | 9.8 | 10.6 | -1.1 |
NM_030820 | COL20A1 | 1.2 | 2.8 | 8.8 | 7.7 | 7.4 | -1.1 |
NM_004994 | MMP9 | 2.4 | 6 | 8.4 | 10.1 | 8.3 | -1.2 |
NM_004926 | BERG36 | 6.5 | 8.1 | 8.2 | 7.7 | 9.9 | -1.4 |
NM_001200 | BMP2 | 15.2 | 13.6 | 8.1 | 4.1 | 10.3 | -1.2 |
NM_015271 | RNF86 | 2.6 | 5.5 | 8.1 | 10 | 7 | -1 |
NM_021952 | ELAVL4 | 7.3 | 8.1 | 8 | 7.9 | 6.8 | -1.1 |
NM_001706 | BCL6 | 7.1 | 8.3 | 7.6 | 7.6 | 19.5 | 1.6 |
NM_001565 | CXCL10 | 1.4 | 1.5 | 7.5 | 12.6 | 23.4 | -1 |
NM_005627 | SGK | 3.4 | 4.9 | 7.5 | 6.6 | 13 | -1 |
NM_007351 | ECM | 3.3 | 7.2 | 7.3 | 8.4 | 8 | 1.1 |
NM_206827 | RASL11A | 1.2 | 4.3 | 7.2 | 6 | 4.5 | 1.2 |
NM_002983 | CCL3 | 8.9 | 8.9 | 7.1 | 8.2 | 197.3 | 1.4 |
NM_003294 | ALPHAII | 2.4 | 4.6 | 7.1 | 9.4 | 8.6 | 1.1 |
NM_153370 | PI16 | 1 | 1.6 | 6.9 | 10.3 | 6.9 | 1 |
NM_003986 | BBH | 1.7 | 3 | 6.8 | 9.8 | 6.6 | -1.2 |
NM_025113 | C13ORF18 | 2.5 | 4.7 | 6.7 | 5.3 | 14.8 | 1.3 |
NM_005449 | TOSO | 3.7 | 8.4 | 6.4 | 6 | 7 | 1.4 |
NM_000389 | P21 | 2.4 | 4.2 | 6.1 | 6.1 | 11.8 | 1.3 |
NM_001001437 | CCL3L3 | 8.5 | 7.8 | 6 | 6.1 | 187 | 1.2 |
NM_001268 | CHC1L | 1.6 | 3.4 | 6 | 6.8 | 4.7 | 1.1 |
NM_206939 | CD20L4 | -1.2 | 2.8 | 5.9 | 8.3 | 6.9 | -2 |
NM_004615 | A15 | 1.2 | 3.5 | 5.8 | 6.3 | 4.8 | -1.3 |
NM_016134 | PGCP | 1.4 | 3 | 5.7 | 7.1 | 5.4 | -1.1 |
NM_005211 | CD115 | 2.2 | 5.6 | 5.6 | 4.8 | 5.1 | 1.7 |
NM_147130 | LY117 | 2.8 | 5.3 | 5.6 | 4.5 | 5.3 | 1.2 |
NM_013445 | GAD | 1.1 | 3.9 | 5.6 | 5.9 | 5 | -1.2 |
NM_007079 | PRL3 | 1.6 | 3.9 | 5.6 | 7.9 | 7.1 | -1.2 |
NM_032199 | ARID5B | 7 | 5 | 5.5 | 5.7 | 6.6 | -2.1 |
NM_001257 | CDH13 | 1 | 2.7 | 5.5 | 5.6 | 5.1 | -1.2 |
NM_001017998 | GNG10 | 2 | 4.3 | 5.5 | 7.4 | 5.3 | 1.5 |
NM_005842 | HSPRY2 | 4.3 | 5.8 | 5.4 | 5.2 | 4.1 | -1 |
NM_016257 | HLP4 | 1.2 | 2.7 | 5.4 | 7 | 5.3 | 1.2 |
NM_052815 | DIF2 | 6.8 | 5.1 | 5.3 | 4.7 | 157.7 | 1.1 |
NM_014862 | ARNT2 | 2.5 | 5.4 | 5.3 | 4.8 | 5.3 | -1 |
Temporal pattern of array gene expression can be categorized
Validity of expression analysis was verified by real timePCR
Illumina array fold change | Real time PCR | |||||||
---|---|---|---|---|---|---|---|---|
Ct | RQ fold * | |||||||
Ref.Seq | Gene Symbol | PMA24 | LPS | VitD3 | Cont | PMA24 | LPS | VitD3 |
Cytokines and Chemokines | ||||||||
NM_002983 | CCL3 | 7.1 | 197.3 | 1.4 | 26 | 27.9 | 776 | 1.6 |
NM_000594 | TNFa | 3 | 121.4 | 1.6 | 29 | 13.9 | 119.4 | 1.1 |
NM_000584 | IL8 | 3.7 | 82.9 | 2.3 | 25 | 1.2 | 222.9 | 3.2 |
NM_000575 | IL1A | 1.1 | 98.7 | -1 | 35 | 5.7 | 2195 | 2.3 |
NM_000576 | IL1B | 2.9 | 75.2 | 1.1 | 26 | 2.5 | 415.9 | 0.7 |
NM_004591 | CCL20 | -1 | 47.6 | 1.1 | 30 | 2.1 | 724.1 | 0.9 |
NM_000600 | IL6 | 3.7 | 29.9 | 2.1 | 28 | 4.6 | 157.6 | 3.5 |
NM_001565 | IP10 | 7.5 | 23.4 | -1 | 30 | 97 | 222.9 | 0.7 |
NM_002089 | CXCL2 | 1.2 | 16.5 | 1.1 | 28 | 0.4 | 48.5 | 1.7 |
NM_002984 | CCL4 | 1.1 | 1.7 | 1.1 | 35 | 52 | 80,000 | 1.9 |
Surface molecules | ||||||||
NM_004233 | CD83 | 1.8 | 10.4 | -1.1 | 23 | 3.2 | 9.8 | 0.6 |
NM_001781 | CD69 | 1.4 | 4.1 | -1.4 | 21 | 3.2 | 4.9 | 0.9 |
NM_000632 | CD11b | 3.3 | 3.1 | 2.7 | 24 | 7.5 | 3 | 2.6 |
NM_000591 | CD14 | -1 | 1.2 | 22.4 | 29 | 1.1 | 1.1 | 45.3 |
Signaling and effector molecules | ||||||||
NM_002423 | MMP7 | 29.9 | 36.5 | -1.4 | 28 | 512 | 181 | 0.6 |
NM_002658 | PLAU | 1.3 | 19.9 | -1 | 28 | 1.1 | 5.3 | 0.6 |
NM_000265 | NCF1 | 18.6 | 17.8 | 3.8 | 29 | 32 | 39.4 | 2.6 |
NM_005627 | SGK | 7.5 | 13 | -1 | 22 | 10.6 | 52 | 1.6 |
NM_000389 | p21 | 6.1 | 11.8 | 1.3 | 25 | 42.2 | 42.2 | 1.1 |
NM_000014 | A2M | 10.4 | 11.5 | 1.1 | 30 | 52 | 32 | 3.2 |
NM_004994 | MMP9 | 8.4 | 8.3 | -1.2 | 30 | 21.1 | 9.2 | 1.1 |
NM_000228 | LAMB3 | 2.9 | 6.5 | 8.5 | 28 | 32 | 19.7 | 64 |
NM_002468 | MYD88 | 4.5 | 4.2 | 1.4 | 27 | 27.9 | 7.5 | 1.5 |
NM_000064 | C3 | 1.8 | 2.3 | -1 | 27 | 119.4 | 42.2 | 1.2 |
NM_003264 | TLR2 | 1.4 | 1.6 | 1.1 | 31 | 11.3 | 3.2 | 2 |
NM_000215 | JAK3 | 1.5 | 1.7 | 1.1 | 18 | 5.7 | 4.9 | 1.4 |
NM_004345 | LL37 | -1.2 | -1.3 | 32.1 | 30 | 1.3 | 0.8 | 84.4 |
NM_001775 | CD38 | -1.9 | -2 | 5.9 | 22 | 1.1 | 0.2 | 7.5 |
NM_001911 | CTSG | -3.4 | -4.8 | -1.3 | 21 | 0.03 | 0.01 | 0.6 |
NM_006573 | TNFSF13B | -4.3 | -5.1 | -1.2 | 22 | 0.3 | 0.1 | 1.9 |
NM_000250 | MPO | -8.3 | -9.6 | -1.1 | 17 | 0.1 | 0.03 | 1.1 |
Transcription factors/Histone modifiers | ||||||||
NM_005384 | NFIL3 | 3.1 | 4.9 | -1.3 | 27 | 9.8 | 78.8 | 3.2 |
NM_000321 | RB1 | 2.2 | 1.8 | 1 | 19 | 3 | 1.1 | -0.2 |
NM_005461 | MAFB | 3.3 | 35.8 | 1.2 | 27 | 17.1 | 18.4 | -1.1 |
NM_005587 | MEF2A | 4 | 4.4 | 1.1 | 19 | 9.2 | 4.3 | 1.1 |
NM_002397 | MEF2C | 1.8 | 1.9 | -1.2 | 19 | 8 | 4.3 | 1.6 |
NM_005920 | MEF2D | 2.1 | 7.9 | -1.1 | 26 | 1.1 | 3 | 0.5 |
NM_021958 | HLX1 | 2.2 | 2.3 | -1 | 23 | 10.6 | 3.5 | 1.2 |
NM_021999 | BRI | 2.6 | 2.2 | -1.2 | 22 | 8.6 | 3.7 | 1.2 |
NM_005474 | HDAC5 | NA | 24 | 4.9 | 4 | 0.8 | ||
NM_012412 | H2AV | NA | 19 | 2.6 | 1 | 1.3 | ||
NM_173158 | Nur77 | 1.2 | 11.7 | 1.1 | 35 | 1.1 | 2.3 | 1 |
NM_001706 | BCL6 | 7.6 | 19.5 | 1.6 | 25 | 78.8 | 34.3 | 8 |
NM_001964 | EGR1 | 4.2 | 13.6 | 1.1 | 27 | 14.9 | 1.2 | 1.4 |
NM_005252 | FOS | 2.4 | 3.3 | -1.5 | 26 | 32 | 2.6 | 0.9 |
NM_002167 | ID3 | 11.9 | 38.9 | 2.7 | 30 | 13 | 18.4 | 8 |
NM_006084 | IRF9 | 2.5 | 2.8 | 1 | 25 | 214.5 | 5.3 | 1.4 |
NM_000399 | EGR2 | 5.3 | 27.3 | 1.1 | 28 | 5.3 | 4.3 | 2.5 |
NM_016270 | KLF2 | 13.9 | 9.8 | -1.3 | 26 | 32 | 97 | 0.5 |
NM_021784 | FOXA2 | 4.9 | 2.9 | -1 | 30 | 73.5 | 16 | 0.3 |
NM_005524 | HES1 | 2.8 | 2.8 | 1.2 | 32 | 27.9 | 64 | 0.8 |
NM_004235 | KLF4 | 1.5 | 1.7 | -1 | 27 | 3.7 | 3 | 1.9 |
NM_002698 | OCT2 | 2.1 | 3.3 | -1.2 | 26 | 14.9 | 7 | 0.4 |
NM_030756 | TCF7L2 | 3 | 2.8 | -1.2 | 21 | 8.6 | 5.3 | 0.5 |
NM_004030 | IRF7 | 2.2 | 2.6 | -1.3 | 26 | 13 | 4.6 | 1.2 |
NM_014707 | HDAC7 | 3.2 | 2.5 | -1.2 | 22 | 29.9 | 16 | 0.7 |
NM_003884 | PCAF | 2 | 1.8 | -1.2 | 25 | 3.7 | 1.4 | 0.8 |
NM_005919 | MEF2B | 1.3 | 1.4 | 1.3 | 27 | 6.5 | 0.4 | 0.8 |
Identification of transcriptional regulators
Cross validation between U937 cells and primary blood monocytes
Ct | ddCt | Ct | ddCt | Ct | ddCt | ||||||
---|---|---|---|---|---|---|---|---|---|---|---|
Ref.Seq | gene | Cont | PMA24 | LPS | Mono* | Macro* | LPS* | Mono* | Macro* | LPS* | |
NM_005587 | MEF2A | 19.1 | -3.2 | -2.1 | 25.2 | -2.4 | -3 | ≥ | 21.2 | -1 | -1.2 |
NM_002397 | MEF2C | 18.9 | -3 | -2.1 | 25.5 | -2.8 | -3 | ≥ | 19.8 | -1.8 | -1.8 |
NM_005920 | MEF2D | 25.5 | -2.4 | -1.6 | 26.4 | -0.7 | -1 | ≈ | 27.7 | -0.8 | -1.5 |
NM_021958 | HLX1 | 22.6 | -3.4 | -1.8 | 24.7 | -2.1 | -2 | ≈ | 24.7 | -2.2 | -2.6 |
NM_021999 | BRI | 22.2 | -3.1 | -1.9 | 26 | -2.9 | -3 | ≈ | 18.9 | -2 | -2.8 |
NM_005474 | HDAC5 | 23.7 | -2.3 | -2.2 | 26.8 | -2 | -2 | ≈ | 25.5 | -1.8 | -2 |
NM_012412 | H2AV | 18.6 | -1.4 | 0.1 | 25.7 | -1.1 | -2 | ≈ | 19 | -0.9 | -1.3 |
NM_173158 | Nur77 | 35 | -0.2 | -1.2 | 33.4 | 0 | -2 | ≈ | 33.5 | -1.7 | -1.2 |
NM_001706 | BCL6 | 24.6 | -6.3 | -5.1 | 27.8 | 0.3 | -1 | ≈ | 20 | -0.3 | -1.3 |
NM_001964 | EGR1 | 26.8 | -3.9 | -0.3 | 30.5 | 0.4 | -5 | ≥ | 22.7 | 8.1 | -2.7 |
NM_005252 | FOS | 25.5 | -5 | -1.4 | 23.7 | 2.8 | -1 | ≈ | 21.6 | 2.7 | -2 |
NM_002167 | ID3 | 29.6 | -3.7 | -4.2 | 31 | 1.2 | 1.1 | ≠ | 23.5 | -2.8 | -2.3 |
NM_006084 | IRF9 | 25.1 | -4.5 | -2.4 | 23.9 | -1.6 | -1 | ≠ | 21.9 | 0.3 | -0.1 |
NM_000399 | EGR2 | 28.2 | -2.4 | -2.1 | 27.7 | 2.6 | 0 | ≤ | 23.8 | 4.4 | -0.7 |
NM_016270 | KLF2 | 26.4 | -5 | -6.6 | 21.7 | 3 | 2.4 | ≈ | 16.7 | 5.1 | 3 |
NM_021784 | FOXA2 | 29.5 | -6.2 | -3.7 | 30.2 | 3.3 | 2.2 | ≈ | 32.3 | 3 | 3 |
NM_005524 | HES1 | 31.5 | -4.8 | -6 | 28 | 6.9 | 2.7 | ≈ | 21.5 | 11 | 9 |
NM_004235 | KLF4 | 26.6 | -3.9 | -1.6 | 22 | 6.5 | 3.9 | ≈ | 20.3 | 4.9 | 4 |
NM_002698 | OCT2 | 25.5 | -3.9 | -2.8 | 22.5 | -0.5 | -1 | ≠ | 19.4 | 0.8 | 1 |
NM_030756 | TCF7L2 | 20.7 | -3.1 | -2.4 | 25 | -0.4 | 0 | ≠ | 20.7 | 1.8 | 1 |
NM_004030 | IRF7 | 26.4 | -3.7 | -2.2 | 25.3 | 0.1 | -1 | ≠ | 23.9 | 1.6 | 1 |
NM_014707 | HDAC7 | 22.2 | -4.9 | -4.2 | 27.8 | 1.4 | 1.1 | ≠ | 22.1 | -0.3 | -0.7 |
NM_003884 | PCAF | 25.1 | -1.9 | 1.5 | 28.1 | 0.7 | 1.2 | ≠ | 28.4 | -0.6 | -0.9 |
NM_005919 | MEF2B | 27.3 | -2.7 | 1.4 | 31.9 | -0.3 | 0 | ≠ | 27.6 | -0.5 | -1.3 |
Primary cells | |||||||||||
U937 cells | donor 1 | donor 2 |