Spatial immune response

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Technology Type

Mass Spectrometry (18)
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ILLUMINA, Illumina HiSeq 2500, NextSeq 500, Nanostring (1)
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Instrument Platform

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Single cells were captured using the 10x Genomics Chromium Controller. (1)
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Epidermal cells : Trypsin dissociation / Dermal cells :MACS Whole Skin Dissociation Kit (1)
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2003 (1)

CHEBI ID

CHEBI:48430 (1)
CHEBI:17822 (1)
CHEBI:16709 (1)
CHEBI:26271 (1)
CHEBI:15356 (1)
CHEBI:22660 (1)
CHEBI:27570 (1)
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CHEBI:15956 (1)
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CHEBI:30746 (1)
CHEBI:17741 (1)
CHEBI:30763 (1)
CHEBI:27266 (1)
CHEBI:17376 (1)
CHEBI:35932 (1)
CHEBI:29016 (1)

Metabolite Name

Histidine (2)
Valine (2)
Choline (2)
Arginine (2)
Tyrosine (2)
Proline (2)
Phenylalanine (2)
Hypoxanthine (2)
TAG 53:6 (C15:0/C16:0/C22:6) (1)
L-3-Methylhistidine (1)
1alpha,24-Dihydroxycholecalciferol (1)
(25S)-1alpha,25,26-Trihydroxyvitamin D3/(25S)-1alpha,25S,26-trihydroxycholecalciferol (1)
Oleoyl (1)
4'-Hydroxynomifensine (1)
Retinamide (1)
Pro Phe Ser (1)
Ile Val Glu His (1)
Eudesmine (1)
Gly Trp (1)
Fukinanolide (1)
Irigenin, dibenzyl ether (1)
N1-(5-Phospho-D-ribosyl)-AMP (1)
Asn Ser Val Phe (1)
Icosa-5,8,11,14-tetraene (1)
Pyridoxal-5-phosphate (1)
L-(-)-Proline (1)
Ser Thr Ile (1)
7-Oxodehydroabietic acid (1)
Dodecylheptaglycol (1)
Androstane-3,7,17-triol (1)

IsPrivate

False (3)

First Public Date

2026 (129)
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2020 (10)
2014 (5)
2019 (4)
2017 (4)
2016 (2)
2015 (2)
2018 (1)

Classification

viruses (1)

Modelling Approach

Agent-based model (1)
Ordinary differential equation model (1)

Study type

Transcription profiling by array (359)
ChIP-seq (105)
RNA-seq of coding RNA (74)
ChIP-chip by array (17)
Other (16)
Methylation profiling by array (16)
Unknown experiment type (15)
RNA-seq of coding RNA from single cells (15)
Methylation profiling by high throughput sequencing (15)
ChIP-chip by tiling array (13)
Proteomic profiling by array (10)
RNA-seq of non coding RNA (9)
Comparative genomic hybridization by array (6)
Spatial transcriptomics by high-throughput sequencing (4)
Transcription profiling by tiling array (3)
RNA-seq of non coding RNA from single cells (2)
Cell line - High-throughput sequencing (2)
RNAi profiling by array (2)
Genotyping by array (2)
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Human - Single-cell sequencing (1)
Cell line - One-color microarray (1)
High-throughput sequencing (1)
Human - One-color microarray (1)
Animal - High-throughput sequencing (1)
Bisulfite-seq (1)
ATAC-seq (1)

Release Date

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2013 (109)
2010 (103)
2015 (92)
2014 (86)
2012 (82)
2020 (72)
2011 (69)
2016 (63)
2026 (55)
2008 (50)
2009 (47)
2019 (44)
2018 (38)
2017 (36)
2007 (17)
2006 (12)
2005 (7)
2004 (5)
2003 (2)
1999 (1)

Lab affiliation

Discovery Proteomics Facility, University of Oxford (2)
Biological Engineering, MIT (1)
Department of Biochemistry, Vanderbilt University, Nashville, TN, USA (1)
Department of Pharmacology and Chemical Biology, Emory University, USA (1)
Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany. NNF Center for Protein Research, Faculty of Health Science, University of Copenhagen, Copenhagen, Denmark. (1)
Department of oncology UNIL CHUV Ludwig Institute for Cancer Research Lausanne Office B25A/04/94 Rue du Bugnon 25a, CH-1005 Lausanne (1)
Department: Department of Microbiology and Immunology Lab: Host and Pathogen Interactivity Lab Institute: National University of Singapore Country: Singapore (1)
Discovery Proteomics Lab, University of Oxford (1)
Max Planck Institute of Biochemistry, Dept. Proteomics and Signal Transduction, Martinsried, Germany (1)
Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany (1)
National Institute for Plant Genome Research Aruna Asaf Ali Marg New Delhi - 110 067 (1)
National Institute of Plant Genome Research Aruna Asaf Ali Marg New Delhi - 110 067 (1)
Proteomics Unit (UCCTs), Instituto de Salud Carlos III, Majadahonda, 28220 Madrid, Spain (1)
School of Medicine, Department of Biochemistry, Emory University (1)
Section/Core Facility Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf (UKE), Martinistr. 52, 20246 Hamburg, Germany (1)
University of Guelph, Department of Molecular and Cellular Biology, 50 Stone Rd. E., Guelph, ON, N1G 2W1 (1)
University of Guelph, Ontario, Canada (1)

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Organotypic microfluidic breast cancer model reveals starvation-induced spatial-temporal metabolic adaptations

BACKGROUND: Ductal carcinoma in situ (DCIS) is the earliest stage of breast cancer. During DCIS, tumor cells remain inside the mammary duct, growing under a microenvironment characterized by hypoxia, nutrient starvation, and waste product accumulation; this harsh microenvironment promotes genomic in...

2019-02-08 | MTBLS669 | MetaboLights

Alcohol-Induced Bone Loss: Driven by Dysregulated Spatial Distribution of Gut Microbiota and PGD2-IL17 Pathway-Mediated Osteoclast Activation

Purpose: Alcohol-induced damage to bone microstructure leads to alcoholic osteopenia (AOP). While prior studies have demonstrated alcohol's negative impact on bone density, the mechanisms by which alcohol induces osteoporosis through immune pathways, gut microbiota dysbiosis, and metabolic altera...

2025-03-28 | MTBLS11887 | MetaboLights

Transcriptional profile of mice with good and poor spatial learning during West Nile virus recovery

Greater than 50% of patients who survive neuroinvasive West Nile virus (WNV), a mosquito-borne, positive-sense strand flavivirus, exhibit cognitive sequelae including memory impairments which may last several years. High survival rates from WNV neuroinvasive disease (WNND) (>90%) have led to hundred...

ORGANISM(S): Mus musculus

2016-06-27 | E-GEOD-72139 | biostudies-arrayexpress

Specific modulation of mucosal immune response, tolerance and proliferation in mice colonized with A. muciniphila

Epithelial cells of the mammalian intestine are covered with a mucus layer that prevents direct contact with intestinal microbes but also constitutes a substrate for mucus-degrading bacteria. To study the effect of mucus degradation on the host response, germ-free mice were colonized with Akkermansi...

ORGANISM(S): Mus musculus

2011-09-20 | E-GEOD-18587 | biostudies-arrayexpress

GeoMx digital spatial profiling on biopsies of triple negative breast cancer patients

In this study, we analyzed the differential spatial transcriptome of Triple-Negative Breast Cancer (TNBC) patients who responded in an opposite manner to neoadjuvant chemotherapy (NACT): we compared responders displaying pathological complete response (pCR) with no-responders who showed disease prog...

ORGANISM(S): Homo sapiens

2023-10-12 | E-MTAB-13069 | biostudies-arrayexpress

Spatial transcriptomics from murine inguinal and mesenteric lymph nodes

B cell-interacting reticular cells (BRC) form transcriptionally and topologically stable immune-interacting microenvironments that direct efficient humoral immunity. While several immune niche factors have been elucidated, the cues sustaining BRC function and topology across activation states remain...

ORGANISM(S): Mus musculus

2023-03-29 | E-MTAB-12468 | biostudies-arrayexpress

Spatial Transcriptomics Unveils Immune Microenvironment Heterogeneity and Response-related Subtypes in NSCLC Treated with Neoadjuvant Chemoimmunotherapy

PRJNA1461882 | ENA

Bcl6 and NFkB cistromes mediate opposing reulation of the innate immune response

Here, using ChIP-seq, we define the NF-κB cistrome which is comprised of 31,070 cis-acting binding sites responsive to LPS-induced signaling. In addition, we demonstrate that the transcriptional repressor B-cell lymphoma 6 (Bcl-6) regulates nearly a third of the Tlr4-regulated transcriptome and tha...

ORGANISM(S): Mus musculus

2010-11-24 | E-GEOD-16723 | biostudies-arrayexpress

Tumor cell heterogeneity drives spatial organization of the intratumoral immune response in squamous cell skin carcinoma

PRJNA994449 | ENA

Spatial omics of acute myocardial infarction reveals a novel mode of immune cell infiltration

Myocardial infarction (MI) continues to be a leading cause of death worldwide. Even though it is well-established that the complex interplay between different cell types determines the overall healing response after MI, the precise changes in the tissue architecture are still poorly understood. Here...

ORGANISM(S): Mus musculus (Mouse)

2025-08-16 | PXD066993 | Pride

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