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Protocols

ImmGen specifications

Information


Unique identifier OMICS_06073
Name ImmGen
Alternative name Immunological Genome Project
Restrictions to use None
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/Immunological_Genome_Project

Taxon


  • Rodents
    • Mus musculus

Maintainer


  • person_outline Joonsoo Kang

Publication for Immunological Genome Project

ImmGen citations

 (43)
library_books

Visceral Adipose Tissue Immune Homeostasis Is Regulated by the Crosstalk between Adipocytes and Dendritic Cell Subsets

2018
PMCID: 5846800
PMID: 29514067
DOI: 10.1016/j.cmet.2018.02.007

[…] errors, thus it will usually be higher than the error implied by taking the standard error of the ΔΔCT values for each replicate.Expression profiling was performed using publicly available raw data (ImmGen GEO: GSE37448) in R (). Between-array RMA quantile normalization was performed and unmapped or multi-mapping probes removed prior to differential expression analysis with limma (). Fold change […]

library_books

Id Proteins Suppress E2A Driven Invariant Natural Killer T Cell Development prior to TCR Selection

2018
Front Immunol
PMCID: 5787561
PMID: 29416542
DOI: 10.3389/fimmu.2018.00042

[…] Raw microarray expression data was requested and downloaded from Immgen for selected subsets: preT_DN3A_Th (DN3a), preT_DN3B_Th (DN3b), T_DN4_Th (DN4), T_DP_Th (DP), T_4SP69+_Th (post-selection CD4SP), NKT_44-NK1_1-_Th (stage 0 and 1 iNKT cells), Tgd_Th (total thym […]

call_split

Antibody Tumor Targeting Is Enhanced by CD27 Agonists through Myeloid Recruitment

2017
Cancer Cell
PMCID: 5734932
PMID: 29198913
DOI: 10.1016/j.ccell.2017.11.001
call_split See protocol

[…] (NA). Seurat: R toolkit for single cell genomics. R package version 1.4.0.) (p < 1 × 10-3 was considered significant). Annotation of the resulting gene lists relative to the coexpression atlas of the Immunological Genome Project () was performed using the on-line ToppGene suite. […]

library_books

The IUPHAR/BPS Guide to PHARMACOLOGY in 2018: updates and expansion to encompass the new guide to IMMUNOPHARMACOLOGY

2017
Nucleic Acids Res
PMCID: 5753190
PMID: 29149325
DOI: 10.1093/nar/gkx1121

[…] ion is difficult for immunologists to access without chemoinformatic expertise not typically present in immunology labs. Immunology is supported by excellent databases—e.g. ImmPort (www.immport.org), ImmGen (www.immgen.org), InnateDB (www.innatedb.ca/), Reactome (www.reactome.org) and IMGT (www.imgt.org)—but these do not provide easy links to pharmacological data. The development of the ‘IUPHAR Gu […]

library_books

Comparison of Transcriptomic Platforms for Analysis of Whole Blood from Ebola Infected Cynomolgus Macaques

2017
Sci Rep
PMCID: 5676990
PMID: 29116224
DOI: 10.1038/s41598-017-15145-7

[…] r system has only a few cell types that can be analyzed and is limited based on its prior information matrix (although this can be modified with additional data). The DCQ approach utilizes the entire Immgen knowledge base to look for over 200 different cell types and can be easily manipulated to use a human background of expression data from isolated cell types. Both platforms correlate well with […]

call_split

Constitutive expression of NF κB inducing kinase in regulatory T cells impairs suppressive function and promotes instability and pro inflammatory cytokine production

2017
Sci Rep
PMCID: 5677020
PMID: 29116141
DOI: 10.1038/s41598-017-14965-x
call_split See protocol

[…] EO with the reference number GSE80757 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc = GSE80757).To generate lists of genes that are regulated between conventional CD4+ T cells and Tregs from the Immgen database, we used the population comparison tool and compared “T_4FP3 + 25 + _Sp” with “T_4FP3-_Sp”, submitted by T. Heng in the Benoist-Mathis lab, Joslin Diabetes Center. We used Venny (http: […]

Citations

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ImmGen institution(s)
Broad Institute of MIT and Harvard, Cambridge, MA, USA

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