Immgen数据库

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

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