Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Single Cell Transcriptomics of peripheral immune cells pre- and post-Immune Checkpoint Blockade

ABSTRACT: Raw sequencing data for magnetically-sorted CD8+ T cells and monocytes from the peripheral blood of eight individuals receiving immune checkpoint blockade (either combination ipilimumab/nivolumab, n=4; or single-agent pembrolizumab, n=4) for the treatment of metastatic melanoma. Samples were taken immediately before the first treatment and 21 days post-treatment. Cells were selected based on positivity for CD8 or CD14 and sorted into single cells using the Chromium (10X Genomics) droplet-based system. Gene expression and V(D)J libraries were prepared in accordance with published protocols before sequencing Illumina HiSeq4000. Analysis of CD8 T cell gene expression and V(D)J features can be found in the associated publication (DOI https://doi.org/10.1101/2020.11.15.383786).

PROVIDER: EGAS00001005507 | EGA |

REPOSITORIES: EGA

ACCESS DATA

Json Xml

Similar Datasets

miRNA signatures of antigen specific CD8+ T cells at different stages of immune response to LCMV infection

Project description:miRNAs play an important role in regulating CD8+ T cell response. We used the microarray approach to profile the miRNA signatures of naïve, day 5 effector, day 8 effector, and memory CD8+ T cells. We identified a miRNA signature associated with rapidly proliferating effector CD8+ T cells. CD8+ T cells from P14 TCR transgenic mice were transferred to C57BL6 recipients which were subsequently infected with LCMV Armstrong. Donor P14 CD8+ T cells were sorted on day 5, day 8, or >day 60 post-infection. Naïve P14 CD8+ T cells were sorted directly from naive P14 splenocytes. The total RNA including miRNAs was extracted from sorted samples, labeled, and hybridized to Agilent Mouse miRNA microarray.

2012-06-04 | E-GEOD-34216 | biostudies-arrayexpress

Gene expression in E14 TG2a cells grown with or without LIF and sorted for 5T4 expression

Project description:E14 TG2a cells grown with LIF were disaggregated and FACS sorted for cell surface 5T4 negativity versus E14 TG2a cells grown without LIF for 3 days and sorted for 5T4 positivity.

2011-02-15 | GSE20372 | GEO

Multiomics characterization of a less invasive microfluidic-based cell sorting technique

Project description:Fluorescence-activated cell sorting (FACS) is a specialized technique to isolate cell subpopulations with a high level of recovery and accuracy. However, the cell sorting procedure can impact the viability and metabolic state of cells. Here, we performed a comparative study and evaluated the impact of traditional high-pressure charged droplet-based and a microfluidic chip-based sorting approach on the metabolic and phosphoproteomic profile of different cell types. While microfluidic chip-based sorted cells more closely resembled the unsorted control group for most cell types tested, the droplet-based sorted cells showed significant metabolic and phosphoproteomic alterations. In particular, greater changes in redox and energy status were present in cells sorted with the droplet-based cell sorter along with higher transcriptional and spliceosomal regulation and mechanical stress signaling. These results indicate microfluidic chip-based sorting is less disruptive compared to droplet-based sorting.

2023-11-09 | MSV000093348 | MassIVE

Transcriptome profiling of influenza-specific memory CD8 T cells following transfer into the airways or in vitro culture

Project description:To examine differences in the transcriptome of resident memory CD8 T cells in the lung, influenza nucleoprotein-specific CD8 T cells from the airways , lung interstitium, lung vasculature, and spleen were FACS sorted and RNA isolated for RNA-seq. In some experiments, FACS sorted cells were transferred into the airways, peritoneum, or in vitro culture before subsequent isolation and RNA isolation.

2020-01-09 | GSE137370 | GEO

10x single cell gene expression and V(D)J immune profiling of T cells from the blood, synovial fluid and synovial tissue in psoriatic arthritis patients

Project description:This study shows the pronounced expansion of CD8 T cell clones at sites of active inflammation within the joints of psoriatic arthritis (PsA) patients compared to blood, and characterises the gene expression of expanded clones using droplet based single cell RNA sequencing. Mononuclear cells were separated from freshly acquired paired peripheral blood and synovial fluid samples from 3 PsA patients using density gradient separation, then enriched for CD4 and CD8 T cells using FACS. Additionally, CD45+ leukocytes were enriched by FACS from the cryopreserved synovial tissue of 2 further PsA patients. All cells were then processed using a 10x Chromium Controller and sequenced by Illumina HiSeq 4000 (peripheral blood / synovial fluid) or NovaSeq with S2 flowcell (synovial tissue).

2020-09-07 | E-MTAB-9492 | biostudies-arrayexpress

Khajanchi2019 - Stability Analysis of a Mathematical Model forGlioma-Immune Interaction under OptimalTherapy

Project description:Stability Analysis of a Mathematical Model for Glioma-Immune Interaction under Optimal Therapy Subhas Khajanchi Abstract We investigate a mathematical model using a system of coupled ordinary differential equations, which describes the interplay of malignant glioma cells, macrophages, glioma specific CD8+T cells and the immunotherapeutic drug Adoptive Cellular Immunotherapy (ACI). To better understand under what circumstances the glioma cells can be eliminated, we employ the theory of optimal control. We investigate the dynamics of the system by observing biologically feasible equilibrium points and their stability analysis before administration of the external therapy ACI. We solve an optimal control problem with an objective functional which minimizes the glioma cell burden as well as the side effects of the treatment. We characterize our optimal control in terms of the solutions to the optimality system, in which the state system coupled with the adjoint system. Our model simulation demonstrates that the strength of treatment u1(t) plays an important role to eliminate the glioma cells. Finally, we derive an optimal treatment strategy and then solve it numerically. Keywords: malignant gliomas; stability analysis; optimal control; adoptive cellular immunotherapy

2024-09-02 | BIOMD0000000891 | BioModels

Single-cell immune repertoire sequencing of B and T cells following infection and autoimmunity

Project description:Single-cell immune repertoire sequencing (gene expression and immune receptor repertoire) was performed under various contexts. This includes CD4 T follicular cells (sorted by surface expression of PD1+ CXCR5+ CD4+) following high dose LCMV clone 13 infection on days 10, 25, and 50 and low dose clone 13 infection on day 10 post infection. We additionally profiled virus-specific CD8 T cells that are specific to either GP33 or NP396. Gp33-specific CD8 T cells were sorted 15 months post infection with either low dose clone 13 LCMV, MCMV-ie2-gp33 or MCMV-m45-gp33. NP396-specific CD8 T cells were isolated either 10 days post challenge or 25 days post challenge using the viral model of dejavu (https://pubmed.ncbi.nlm.nih.gov/16604192/). B and T cells were isolated 14 days post induction of Experimental autoimmune encephalomyelitis (EAE).

2022-02-01 | E-MTAB-11330 | biostudies-arrayexpress

Single-cell transcriptome atlas reveals the underlying mechanism of kynurenic acid in regulation tumor immune microenvironment in glioblastoma

Project description:We performed 4D-DIA approach to quantified the proteome of GBM tissues from two groups. An average of 8880 quantified proteins were identified in each sample. In order to further explore the regulation of Kyna on GMB-resident T cells at the protein level, we performed 4D-DIA proteome analysis of CD45+Cd3e+CD8+ cells sorted from GMB in Kyna-treated mice and control mice.

2025-10-30 | PXD070137 |

PAX5 transduction of Pax5-/- pro-B cells

Project description:After 5 days in culture with 2ng/ml of IL7, Pax5-/- transduced pro-B cells with PAX5A or PAX5B cDNA were sorted according to their EGFP positivity and total RNA was extracted.

2018-09-01 | GSE104890 | GEO

Massively parallel single-cell chromatin landscapes of human immune cell development and intratumoral T cell exhaustion

Project description:Understanding complex tissues requires single-cell deconstruction of gene regulation with precision and scale. Here we present a massively parallel droplet-based platform for mapping transposase-accessible chromatin in tens of thousands of single cells per sample (scATAC-seq). We obtain and analyze chromatin profiles of over 200,000 single cells in two primary human systems. In blood, scATAC-seq allows marker-free identification of cell type-specific cis- and trans-regulatory elements, mapping of disease-associated enhancer activity, and reconstruction of trajectories of differentiation from progenitors to diverse and rare immune cell types. In basal cell carcinoma, scATAC-seq reveals regulatory landscapes of malignant, stromal, and immune cell types in the tumor microenvironment. Moreover, scATAC-seq of serial tumor biopsies before and after PD-1 blockade allows identification of chromatin regulators and differentiation trajectories of therapy-responsive intratumoral T cell subsets, revealing a shared regulatory program driving CD8+ T cell exhaustion and CD4+ T follicular helper cell development in association with clinical response. We anticipate that droplet-based single-cell chromatin accessibility will provide a broadly applicable means of identifying regulatory factors and elements that underlie cell type and function.

2019-04-16 | GSE129785 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data