Expression data is for primary human and murine neutrophils and PLB985 or HL60 cells before and after differentiation with either 1.3% DMSO or 1.3% DMSO + 0.5% Nutridoma-CS (Sigma). Data for PLB985 and HL60 cells is our own RNA-Seq data. Raw data for primary human and mouse neutrophils was collated from previously published studies and analyzed along-side our own1-6. For convenience, links to Dictyostelium discoideum homologs are also displayed. .
Reference:
Rincon E, Rocha-Gregg BL, and Collins SR. A map of gene expression in neutrophil-like cell lines. 2018. BMC Genomics [Full text] [PubMed]
Navigating the data
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The gene symbols have clickable links that direct to the corresponding NCBI Gene page.
Search: Data may be searched by symbol, Gene ID or protein domain and sorted by any column.
Expression Values: Expression values are FPKM normalized on a log10 scale. Transcripts that were undetected were assigned an arbitrary value of -4.00. In general, negative values correspond to low transcript levels. Values above zero correspond to genes that are expressed at varying levels, and values above two correspond to highly expressed genes. As the values are on a log10 scale, a difference of 1 for the same gene between two samples corresponds to a 10-fold difference in expression at the transcript level.
Gene Expression in Neutrophil-like Cell Lines
| Symbol | GeneID | Primary Human | PLB985 Undiff | PLB985 +DMSO | PLB985 +Nutri | HL60 Undiff | HL60 +DMSO | HL60 +Nutri | Mouse_Homolog | Mouse | Dicty_Homolog | Prot_Domain |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| TSPAN6 | 7105 | -2.18 | -4.00 | -4.00 | -4.00 | -4.00 | -4.00 | -4.00 | Tspan6 | -0.91 | - | 4HB_MCP_1|Tetraspannin |
| TNMD | 64102 | -4.00 | -4.00 | -4.00 | -4.00 | -4.00 | -4.00 | -4.00 | Tnmd | -4.00 | - | BRICHOS |
| DPM1 | 8813 | 1.41 | 1.72 | 1.58 | 1.57 | 1.75 | 1.55 | 1.60 | Dpm1 | 0.75 | dgtB | Glyco_tranf_2_2|Glyco_tranf_2_3|Glyco_transf_21|Glycos_transf_2 |
| SCYL3 | 57147 | 0.76 | 0.34 | 0.54 | 0.55 | 0.25 | 0.45 | 0.40 | Scyl3 | 1.02 | - | Pkinase|Pkinase_Tyr |
| C1orf112 | 55732 | 0.40 | 0.97 | 0.18 | 0.26 | 0.77 | 0.03 | 0.20 | BC055324 | 0.28 | - | DUF4487|Sec23_helical |
| FGR | 2268 | 2.73 | 0.02 | 0.51 | 0.89 | 0.79 | 1.44 | 1.34 | Fgr | 2.31 | - | Pkinase|Pkinase_Tyr|SH2|SH3_1|SH3_2|SH3_9 |
| CFH | 3075 | -1.09 | -4.00 | -4.00 | -4.00 | -4.00 | -4.00 | -2.20 | Cfh | 0.07 | - | Sushi |
| FUCA2 | 2519 | 0.49 | -2.54 | -4.00 | -2.74 | 0.57 | 0.52 | 0.85 | Fuca2 | 1.71 | - | Alpha_L_fucos|Fucosidase_C |
| GCLC | 2729 | 0.61 | 1.51 | 1.63 | 1.49 | 1.46 | 1.64 | 1.70 | Gclc | 0.25 | gcsA | GCS |
| NFYA | 4800 | 1.50 | 1.05 | 1.09 | 1.16 | 0.93 | 0.98 | 1.14 | Nfya | 1.23 | - | CBFB_NFYA |
| Symbol | GeneID | Primary Human | PLB985 Undiff | PLB985 +DMSO | PLB985 +Nutri | HL60 Undiff | HL60 +DMSO | HL60 +Nutri | Mouse_Homolog | Mouse | Dicty_Homolog | Prot_Domain |
- Jiang K, Zhu L, Buck MJ, Chen Y, Carrier B, Liu T, et al. Disease-Associated Single-Nucleotide Polymorphisms From Noncoding Regions in Juvenile Idiopathic Arthritis Are Located Within or Adjacent to Functional Genomic Elements of Human Neutrophils and CD4+ T Cells. Arthritis Rheumatol. [Internet]. 2015 [cited 2017 Jul 3];67:1966–77. Available from: http://www.ncbi.nlm.nih.gov/pubmed/25833190
- Wright HL, Thomas HB, Moots RJ, Edwards SW. RNA-seq reveals activation of both common and cytokine-specific pathways following neutrophil priming. PLoS One [Internet]. 2013 [cited 2015 Sep 16];8:e58598. Available from: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0058598
- Thomas HB, Moots RJ, Edwards SW, Wright HL. Whose gene is it anyway? the effect of preparation purity on neutrophil transcriptome studies. PLoS One. 2015;10:1–15.
- Cusanovich DA, Daza R, Adey A, Pliner HA, Christiansen L, Gunderson KL, et al. Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing. Science (80-. ). [Internet]. 2015 [cited 2017 Jul 3];348:910–4. Available from: http://www.ncbi.nlm.nih.gov/pubmed/25953818
- Taylor A, Tang W, Bruscia EM, Zhang PX, Lin A, Gaines P, et al. SRF is required for neutrophil migration in response to inflammation. Blood. 2014;123:3027–36.
- Coffelt SB, Kersten K, Doornebal CW, Weiden J, Vrijland K, Hau C-S, et al. IL-17-producing γδ T cells and neutrophils conspire to promote breast cancer metastasis. Nature. 2015;522:345–8.