Table 1.
Application of “Omics technologies” in complex NK cell research.
| Species | Sample | Method | Keypoint | Reference |
|---|---|---|---|---|
| Transcriptomics: microarray related studies in NK cells (mRNA/miRNA/LncRNA) | ||||
| Mo | NK. Sp./Lv./SI. | P: Affymetrix MoGene 1.0 ST array | 1. ILC1. Lv.: CD49a+, TRAIL+ | GSE37448 (15) |
| 2. ILC1. SP.: CD127+, Eomes− | ||||
| 3. ILC1. SI.: CD27−, Eomes− | ||||
| ILC1. Sp./Lv./SI. | A: GenePattern; PCA | |||
| Mo | NK. Sp. Healthy | P: Affymetrix MoGene 1.0 ST array | Zbtb32 controls expansion of virus-specific NK | GSE15907 (13) |
| NK. Sp. MCMV | A: GenePattern | |||
| Hu | NK. PB./CB./D. | P: Whole HuGenome Oligo Microarray | 1. Homeobox TFs enrich in dNK | GSE24268 (14) |
| A: Agilent’s Feature-Extraction v 9.1.3 | 2. Zinc-finger TFs enrich in pNK; | |||
| Hu | NK. PB./CB./D. | P: Hu miRNA microarray | 1. Inhibitory miRNA: miR-483-3p | GSE66325 (16, 17) |
| A: Agilent’s Feature-Extraction v 9.5.3.1 | 2. Activated miRNA: miR-362-5p | |||
| Hu | NK. PB./CB./D. | P: Agilent Hu180K lncRNA and mRNA microarray | Lnc-CD56 upregulates CD56 | (18) |
| Transcriptomics: mRNA-seq-related studies in NK cells | ||||
| Mo | CD49a+ NK. Lv./Sp./BM. | P: HiSeq 2500 | 1. trNK: CD49a+, CD69+ | (19) |
| DX5+ NK. Lv./Sp./BM. | A: ESAT software | 2. trNK is depend on T-bet | ||
| Transcriptomics: scRNA-seq-related studies in NK cells | ||||
| Hu | ILCs. Tn | L: SMART-seq2 Pro. | 1. Human ILCs express RARG | (20) |
| P: HiSeq2000 | ||||
| NK. Tn | A: STAR v2.3.0, SCDE | 2. Mature ILCs including NK cells express PLZF, unlike mice | ||
| Mo | WT. CLP. | L: SMART-seq2 Pro. | PD-1+ ILCP | (21) |
| Bcl11b−/−. CLP. | P: HiSeq2000; A: DESeq2, SPADE | |||
| Transcriptomics: miRNA-seq-related studies in NK cells | ||||
| Mo | NK. Sp. Resting | P: GA (Illumina) seq; SOLiD seq | Inhibitory miRNA: miR-223 | GSE21003 (22) |
| NK. Sp. IL-15-activated | A: pipeline v 0.2.2, SHRiMP | |||
| Transcriptomics: ATAC-Seq related studies in NK cells | ||||
| Mo | NK. Sp./Lv. | ATAC-Seq, P: HiSeq 2500 | Regulomes of ILCs VS T cells: | GSE77695 (23) |
| ILC1. Lv. | A: MACS v 1.4.2, HOMER v 4.8 | |||
| HSC. BM. | ChIP-Seq, P: HiSeq 2500 | 1. The regulator of the ILC effector genes is easier to open | ||
| CLP. BM. | A: SICER, MACS v 1.4.2 | |||
| NKp. BM. | RNA-seq, P: HiSeq 2000 | 2. Regulomes of ILCs arborize early at precursor stages | ||
| imNK. BM. | A: Cufflinks 2.2.1 | |||
| Proteomic: CyTOF-related studies in NK cells | ||||
| Hu | NK. CB./PB. Healthy | P: Mass cytometer (Fluidigm) | The increased diversity of NK cells affects the function | (24) |
| NK. PB. HIV | A: Inverse Simpson Index | |||
| Hu | NK. PB. | P: Mass cytometer (Fluidigm) | CD49e− trNK in human liver | (25) |
| NK. L-PxF. | A: SPADE; Cytobank | |||
| Proteomic: LC-MS/MS-related studies in hematopoietic cells (focused on NK cells) | ||||
| Hu | CD56bright NK. PB. | P: UHPLC, Q Exactive HF | The effect genes of NK and TEM cells are similar | PXD004352 (26) |
| CD56dim NK. PB. | A: MaxQuant v1.5.3.2, Communication | |||
| CRISPR-related studies in NK cells | ||||
| Mo | SFRs−/− NK. | P: CRISPR | SFRs for NK cell education | (27) |
| A: Sequencing; FACS | ||||
Mo, mouse; Hu, Human; Sp, spleen; Lv, Liver; BM, bone marrow; SI, small intestinal lamina propria; L-PxF, liver postexcision flush; PB, peripheral blood mononuclear cell; CB, cord blood mononuclear cells; D, decidual mononuclear cells; Tn, tonsil; SFRs, signaling lymphocytic activation molecule family receptors library preparation; TFs, transcription factors; HSCs, hemopoietic stem cells; CLP, common lymphoid progenitors; trNK, tissue-resident natural killer; NKp, natural killer cell precursor; imNK, immature natural killer; cNK, conventional natural killer; ILCP, precursors of innate lymphoid cells; L, library preparation; P, platform; A, analysis; Pro., protocol; scRNA-seq, single-cell RNA sequencing; ATAC-Seq, assay for transposase-accessible chromatin sequencing; ChIP-seq, chromatin immunoprecipitation sequencing; CyTOF, cytometry by time of flight; LC-MS/MS, liquid chromatography–tandem mass spectrometry; CRISPR, clustered regularly interspaced short palindromic repeats; SCDE, single-cell differential expression; SPADE, spanning-tree progression analysis of density-normalized events; SICER, Spatial clustering for identification of ChIP-enriched regions; UHPLC, ultra-high performance liquid chromatography; CD, cluster of differentiation; dNK, decidual natural killer; pNK, peripheral natural killer; RNA-seq, RNA sequencing; ILC, innate lymphoid cell; IL, interleukin; ncRNA, non-coding RNA; FACS, fluorescence-activated cell sorting; HIV, human immunodeficiency virus; MCMV, murine cytomegalovirus.