Immgen（Immunological Genome Project）
website：https://www.immgen.org/
Heng TS, et al, Immunological Genome Project Consortium. Nat Immunol. 2008 10 : 1091.
此数据库存储了mouse免疫细胞的基因表达信息，包含microarray和RNAseq数据集。
数据集
数据集下载链接
http://rstats.immgen.org/DataPage/
| Name | GEO Accession | Description | Cell Types | Pubmed | Normalized Tables | Raw Gene Count Table |
|---|---|---|---|---|---|---|
| Name | GEO Accession | Description | Cell Types | Pubmed | Normalized Tables | Raw Gene Count Table |
| ImmGen ULI: Deep RNA-seq data | GSE122597 | Five highly purified immunocyte populations profiled to unusual depth as multiple replicates (8 to 16). Suitable for exploration of genes expressed at very low levels. | NK Cells, Follicular B, Naive CD4+ abT, gdT cells and peritoneal macrophages. | GSE122597 Normalized Gene table | GSE122597 Raw Gene Count table | |
| ImmGen ULI: Systemwide RNA-seq profiles (#1) | GSE109125 | 83 populations representing all lineages and several differentiation cascades prepared from unchallenged mice and after LPS, anti-CD3, viral infection cell activation. | B Cells, Stromal Cells, Dendritic Cells, Granulocytes, Innate Lymphocytes, Stem Cells, Macrophages, ab T Cells, gd T Cells | 30686579 | GSE109125 Normalized Gene table | GSE109125 Raw Gene Count table |
| ImmGen ULI: OpenSource Mononuclear Phagocytes Project | GSE122108 | 130 populations comprising progenitors, residents, and stimulated (C.alb, LPS, injury, APAP+ starved overnight and pIC) mononuclear phagocytes for OpenSource MNP Project. | Macrophages, Kupffer Cell/Macrophages, Dendritic Cells, Microglia, Monocytes. | 27327993 | GSE122108 Normalized Gene table | GSE122108 Raw Gene Count table |
| ImmGen ATAC-seq data | GSE100738 | Chromatin accessibility on 86 primary immune cell types, directly ex vivo, used to map out the atlas of cis-regulatory elements of the immune system. | Epithelial Cells, Thymocytes, gd T Cells, Neutrophil, NK Cells, CD4 Naive T Cell, CD4 Treg Cell, CD8 T Cells, CD8 Naive T Cells B Cells, NKT Cells, Innate Lymphocytes, Monocytes, Macrophages, Dendritic Cells, Microglia, Stromal Cells, Stem Cell | 30686579 | Not Applicable | Not Applicable |
| ImmGen Microarray Phase 1 | GSE15907 | 178 populations compromiing of gene-expression microarray datasets ("version1" labeling) from primary cells from multiple immune lineages are isolated ex-vivo, primarily from 6weeks B6 male mice. | gd T Cells, ab T Cells, Dendritic Cells, Macrophages, Stem Cells, B Cells, Stromal Cells, Neutrophils, Fibroblast, NK Cells, NK T Cells, Monocytes, CD4 Naive T Cell. | 23382184 23023392 23098840 PMC3572860 22797772 22466668 22473038 PMC3140206 18800157 [ PMC3761616](https://www.ncbi.nlm.nih.gov/pubmed/ PMC3761616) | GSE15907 Normalized Data | Not Applicable |
| ImmGen Microarray Phase 2 | GSE37448 | 82 populations compromising of gene-expression microarray datasets ("version2" labeling) from primary cells from multiple immune lineages are isolated ex-vivo, primarily from 6weeks B6 male mice. Complements the V1 compendium with additional cells. Unfortunately, the version change in the labeling process, while more efficient, introduced some biases such that the two sections of the data can be compared grossly, but not at fine resolution (we tried...). | gd T Cells, ab T Cells, Dendritic Cells, Macrophages, Stem Cells, B Cells, Stromal Cells, Neutrophils, Fibroblast, NK Cells, NK T Cells, Monocytes, CD4 Naive T Cell. | 24801837 | GSE37448 Normalized Data | Not Applicable |
| ImmGen ULI RNA-seq data | GSE127267 | Superseries: Primary RNAseq data from carefully sorted immunocyte populations, sequenced using ImmGen's SOP for 'ultra-low-input' population RNAseq (typically 500 to 1,000 cells) performed by Smartseq2. | B cells, Dendritic Cells, Stromal Cells, Granulocytes, Innate Lymphocytes, Macrophages, ab T Cells, Monocytes, Macrophages | Not Applicable | Not Applicable | |
| Cell specific response to IFNa | GSE75202 | Early responses to IFNa (Type-1 interferon) in 11 different immunocyte populations in the mouse (core ImmGen first generation 11-cell set). Profiles from these were used to analyze cell specific responses to IFNa. In general a core set of ISG transcripts are induced in all cells. Smaller sets of ISGs were induced in a cell specific manner. In particular, splenic granulocytes and dendritic cells show a specific induction of additional sets of ISGs. | ab T cells, macrophages, Granulocytes, B Cells, Innate Lymphocyte, Dendritic Cell, Regulatory T Cells, gd T cells | 26824662 | GSE75202 Normalized Data | Not Applicable |
| Peritoneal cavity macrophage response to IFNg and IFNa | GSE110549 | We seeked to determine in vivo effects of IFNg and IFNa response in peritoneal cavity macrophages. These cells were part of ImmGen Interferon cytokine study and immunocytes were sorted according to Immgen's standard lineage panel. Profiles from peritoneal cavity macrophages were used to analyze cell specific responses to IFNg. | Macrophages | 26824662 | GSE110549 Normalized Data | Not Applicable |
| ImmGen Cytokines: Interferons | GSE75306 | Superseries: Microarray data from a detailed study of responses to Type-1 interferons in vivo, across many immunoyte lineages, as a detailed time-course in B cells, or assessing the effect of mutations in signal transduction molecules) | Not Applicable | Not Applicable | ||
| Gene expression data for 39 inbred mice strains for neutrophils | GSE60336 | Genome-wide expression data were generated for polymorphonuclear neutrophils (granulocytes, GN) across 39 inbred mouse strains of the Mouse Phenome Databse "Priority Strain Panel". | Granulocytes | 25267973 | GSE60336 Normalized Data | Not Applicable |
| Gene expression data for 39 inbred mice strains for CD4+ T cells | GSE60337 | Genome-wide expression data were generated for CD3+CD4+CD62L+ naive T splenocytes across 39 inbred mouse strains of the Mouse Phenome Databse "Priority Strain Panel" | CD4+ T Cells | 25267973 | GSE60337 Normalized Data | Not Applicable |
| ImmGen ULI: Male-Female Immune Differences | GSE124829 | 11 diverse immunocyte populations from male and female mice of varying ages stimulated with different dose of IFN to understand the immune system's sexual differences. | B Cells, Dendritic Cells, Neutrophils, Macrophages, Natural Killer T Cells, ab T Cells, gd T Cells, Microglia, Regulatory T Cells. | 30686579 | GSE124829 Normalized Gene table | GSE124829 Raw Gene Count table |
| Kinetics of IFNa response | GSE75195 | We describe finely resolved kinetics of the transcriptional response to IFNa in B cells in vivo. Temporal changes in expression of the most robustly induced ISGs were analyzed across 23 (15min - 15hrs) timepoints. Most ISGs reach peak induction at approximately 2hrs and generally in a synchronus manner. These analses provide insight into the regulatory network structure of IFN responses. | B Cells | 26824662 | GSE75195 Normalized Data | Not Applicable |
| IFNa dose response in primary murine B cells | GSE75194 | B cells respond robustly to IFNa. Here we analyze gene expression profiles of primary murine splenic B cells treated with 10 fold serially diluted IFNa in vitro. We explore sensitivity to ISGs to IFNa as they relate to dose. Generally ISGs do not cluster significantly in a dose dependent manner. However there are notable spreads in sensitivity to IFNa. | B Cells | 26824662 | GSE75194 Normalized Data | Not Applicable |
| Dependency of ISG expression on IFNAR1 and Tyk2 | GSE75203 | We analyze the expression profile of ISGs in the context of IFNAR1-KO primary murine B cells and macrophages. These analses were used to define ISG gene sets that are under tonic control. Furthermore, these analyses enabled the definition of ISGs that are dependent on Tyk2 signaling. | B Cells, Macrophages, CD4+ T Cells | 26824662 | GSE75203 Normalized Data | Not Applicable |
| Genome-wide profilings of IFN-stimulated murine splenic B cells by ATAC-Seq | GSE75262 | We report the IFN-induced dynamics in murine splenic B cells. Male C57BL/6 mice were injected subcutaneously with 10,000U IFNa and spleens were removed at 90min. B cells were negatively isolated using magnetic beads and profiled for the chromatin configuration by ATAC-seq. | B Cells | 26824662 | Not Applicable | Not Applicable |
| Genome-wide profilings of IFN-stimulated murine splenic B cells by ChIP-seq | GSE75250 | We report the IFN-induced dynamics in murine splenic B cells. Male C57BL/6 mice were injected subcutaneously with 10,000U IFNa and spleens were removed at designated time. B cells were negatively isolated using magnetic beads and profiled for the binding of PolII and Stat2 by ChIP-seq analysis. | B Cells | 26824662 | Not Applicable | Not Applicable |
| Cell specific response to IFNg | GSE112876 | Early responses to IFNg (Type-2 interferon) in 11 different immunocyte populations in the mouse (core ImmGen first generation 11-cell set). Profiles from these were used to analyze cell specific responses to IFNg. | B cells, Dendritic Cells, Granulocytes, Macrophages, Innate Lymphocytes, ab T Cells, gd T Cells, Regulatory T cells | 26824662 | GSE112876 Normalized Data | Not Applicable |
| Gene expression data for 39 inbred mice strains for neutrophils and CD4+ T cells | GSE60338 | Superseries:composed of the SubSeries, 60336 and GSE60337 | neutrophils, CD4+ T cells | 25267973 | Not Applicable | Not Applicable |
