Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

14 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Mapping the developing human immune system across organs - VDJ-seq

ABSTRACT: We profiled hematopoietic, lymphoid and peripheral fetal organs to systematically assess the heterogeneity of antigen receptors in immune cell populations across human tissues during development. Single-cell suspensions were obtained from fresh tissue. Cells were either DAPI-CD45+ or DAPI-CD45- FACS-isolated cells, or unsorted.

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Homo sapiens

SUBMITTER: Emma Dann

PROVIDER: E-MTAB-11388 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Mapping the developing human immune system across organs - scRNA-seq

Project description:We profiled hematopoietic, lymphoid and peripheral fetal organs to systematically assess the heterogeneity of immune cell populations across human tissues during development. Single-cell suspensions were obtained from fresh tissue. Cells were either DAPI-CD45+ or DAPI-CD45- FACS-isolated cells, or unsorted.

2022-05-12 | E-MTAB-11343 | biostudies-arrayexpress

A single-cell atlas of lymphocyte adaptive immune repertoires and transcriptomes reveals age-related differences in convalescent COVID-19 patients

Project description:We utilize single-cell sequencing (scSeq) of lymphocyte immune repertoires and transcriptomes to quantitatively profile the adaptive immune response in COVID-19 patients of varying age. Our scSeq analysis defines the adaptive immune repertoire and transcriptome in convalescent COVID-19 patients and shows important age-related differences implicated in immunity against SARS-CoV-2.

2021-03-20 | E-MTAB-10169 | biostudies-arrayexpress

Early human lung immune cell development and its role in epithelial cell fate

Project description:In this work, we collected CD45-enriched human lung cells from 6 to 22 week post conception (pcw) and built a single-cell transcriptomic and proteomic cell atlas.. At the embryonic stage, we observed an early wave of innate immune cells, including ILCs, NK, myeloid cells and lineage progenitors. By the canalicular stage, we detected naive T lymphocytes high in cytotoxicity genes, and mature B lymphocytes, including B1 cells. Our analysis suggests that fetal lungs provide a niche for full B cell maturation. Given the abundance of immune cells, we investigated their possible effect on epithelial maturation and found that IL-1β drives epithelial progenitor exit from self-renewal and differentiation to basal cells in vitro. In vivo, IL-1β-producing myeloid cells were found adjacent to epithelial tips, suggesting that immune cells may direct the developing lung epithelium.

2022-12-09 | E-MTAB-11528 | biostudies-arrayexpress

Single-cell RNA-Seq of entire ventricles of C57BL/6J and B6.Rag2del mice after myocardial infarction

Project description:We compared the cellular and molecular outcome following permanent LAD ligation in wildtype and T- and B cell deficient Rag2del mice. Our results demonstrate that the significant changes in the cardiac immune response following myocardial infarction (MI). 8-12 weeks old, male and female C57BL/6J mice (Charles River, Wilmington, MA, USA) and B6.Rag2del mice (Jackson laboratory, Bar Harbor, ME, USA) were used for this study. Seven days after MI, entire mouse ventricles were isolated and enzymatically digested. Cells were then labelled with CD45 magnetic beads (Miltenyi Biotec, Germany) and positively enriched using the AutoMACS instrument (Miltenyi Biotec, Germany). Viable macrophages/monocytes (CD45+CD11b+CD11c-DAPI-Lactadherinlo), dendritic cells (CD45+CD11b+CD11c+ DAPI-Lactadherinlo), and NK cells (CD45+CD11b-CD11c+NK1.1+ DAPI-Lactadherinlo) were then sorted on the BD FACSAriaTM IIIu (Becton Dickinson, Franklin Lakes, NJ, USA) roughly in a 1:1:1 ratio into DMEM containing 10% FCS before processing for 10× Genomics single-cell RNA sequencing (scRNA-Seq). Libraries for scRNA-Seq were constructed according to the 10× Genomics protocol using the GemCode Single-Cell 3′ Gel Bead and Library V3 Kit. Quality of amplified cDNA and final libraries were evaluated on the 2100 Bioanalyzer instrument (Agilent) using a High Sensitivity NGS Analysis Kit (Advanced Analytical). Subsequent sequencing was conducted on the HighSeq4000 Sequencing System using the HiSeq SBS and HiSeq PE Cluster Kit V4 (all Illumina, San Die-go, CA. USA).

2023-07-20 | E-MTAB-13147 | biostudies-arrayexpress

scRNA-seq of stromal, tumor and immune cells from EMT6 tumors treated with aTGFb/aPD-L1

Project description:We performed 10x single cell RNA-seq on sorted populations: T cell (7AAD- Calcein blue+ CD45+ THY1.1- TCRb+), fibroblasts (7AAD- Calcein Blue+ CD45- THY1.1- CD31- PDPN+), myeloid cells (7AAD- Calcein Blue+ CD45+ THY1.1- CD11b+) and tumor cells (7AAD- Calcein Blue+ CD45- THY1.1+) from cells in an orthotopic EMT6 tumor model 7 days after treatment initiation in four experimental groups: 1) Control 2) aPD-L1 3) aTGFb 4) aPD-L1 and aTGFb.

2023-06-30 | E-MTAB-13072 | biostudies-arrayexpress

Single cell TCR-seq profiling of T cells isolated from LNs of MC38 tumor-bearing mice

Project description:We investigate the single-cell landscape of the inflammatory mouse tumor model MC38, a C57BL/6 tumor cell line derived from colon adenocarcinoma. MC38 (diluted in HBSS and matrigel) was inoculated in the right unilateral flank (in the border of positions B2 and B3) of C57BL/6 mice (ref Study 16-3384 AV). Draining lymph nodes were taken one day after group-out (average 150-250 mm3 tumor size at day 0), approximately 14-19 days. Draining lymph nodes were dissociated and flow sorted accordingly to obtain the cells for 10x Chromium 5' Gene Expression Profiling and TCR sequencing.

2022-08-16 | E-MTAB-9734 | biostudies-arrayexpress

A cell atlas of human thymic development defines T cell repertoire formation

Project description:We performed single-cell RNA-sequencing to create a cell census of the human thymus during development, early childhood and adult life. We sampled 15 embryonic and fetal thymi spanning thymic developmental stages between 7 post-conception weeks (PCW) to 17 PCW, and 9 postnatal thymi from paediatric and adult samples. We compared the cellular composition and T cell differentiation within human and mouse thymus using newly generated and repository mouse datasets. Finally, we investigated the bias in the recombination and selection of human versus mouse TCR repertoires.

2020-02-21 | E-MTAB-8581 | biostudies-arrayexpress

Single cell RNA-seq profiling of T cells isolated from MC38 mouse tumors

Project description:We investigate the single-cell landscape of the inflammatory mouse tumor model MC38, a C57BL/6 tumor cell line derived from colon adenocarcinoma. MC38 (diluted in HBSS and matrigel) was inoculated in the right unilateral flank (in the border of positions B2 and B3) of C57BL/6 mice (ref Study 16-3384 AV). Tumors were taken one day after group-out (average 150-250 mm3 at day 0), approximately 14-19 days. Tissues were dissociated and flow sorted accordingly to obtain the following groups for 10x Chromium 5' Gene Expression Profiling. Our results indicate that the degree of clonal expansion is correlated with expression of T cell exhaustion markers, and that T cells with strong exhaustion phenotype also express high levels of activation markers, such as interferon gamma.

2019-05-12 | E-MTAB-7919 | biostudies-arrayexpress

Single cell RNA-seq profiling of T cells isolated from LNs of MC38 tumor-bearing mice

2021-02-16 | E-MTAB-9274 | biostudies-arrayexpress

scRNAseq of small intestine-derived lamina propria CD45+ cells from untreated wild type (WT), untreated intestinal epithelial specific LSD1 knockout (cKO), antibiotic-treated WT mice and antibiotic-treated cKO mice

Project description:Mice with an intestinal epithelial specific knockout of LSD1 have changes in the intestinal epithelium including loss of Paneth and Goblet cells along with a general status of epithelial immaturity. To assess the influence of these epithelial specific changes on the mucosal immune system we performed a scRNAseq on CD45+ immune cells from the small intestine of mice with an epithelial specific LSD1 deletion (Villin-Cre+; Lsd1f/f) and wild type mice (Villin-Cre -; Lsd1f/f). To rule out a possible influence of the bacterial microbiome in the observed changes in CD45+ cell types we performed the same experiment in mice treated with antibiotics. These data allowed us to pinpoint changes in the cell populations of the mucosal immune system upon loss of LSD1 in the intestinal epithelium such as IgA producing cells and ILCs.

2023-08-02 | E-MTAB-10492 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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