Analysis of thymic dendritic cells (DCs) subtypes from Foxn1cre x ROSA26TdTOMATO mice by single cell transcription profiling.
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB33083 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR3379610_1.fastq.gz | Fastqsanger.gz | |||
| ERR3379610_2.fastq.gz | Fastqsanger.gz | |||
| ERR3379611_1.fastq.gz | Fastqsanger.gz | |||
| ERR3379611_2.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 4 of 4 |
Similar Datasets
Project description:Thymi from Foxn1cre x ROSA26TdTOMATO were enzymaticaly digested, cells were MACS enriched for CD11c+ fraction. Dendritic cells were then FACS sorted (BD influx sorter) as Gr-1-CD11c+TdTOMATO+. TdTOMATO DCs represent fraction of thymic DCs which acquire antigen (TdTOMATO) from thymic epithelial cells, through the process of antigen transfer.
2020-03-20 | E-MTAB-8028 | biostudies-arrayexpress
Project description:Analysis of thymic dendritic cells (DCs) subtypes from Foxn1cre x ROSA26TdTOMATO mice by single cell transcription profiling.
| PRJEB33083 | ENA
Project description:Thymic antigen-presenting cells (APCs), including thymic dendritic cells (t-DCs) and medullary thymic epithelial cells (mTECs) have been described to play a critical role in thymic Treg generation. Our findings could show that both these thymic APCs can induce a more pronounced demethylation of Foxp3 and other Treg-specific epigenetic signature genes in developing Tregs when compared to splenic DCs. In order to elucidate the unique properties of thymic APCs, gene expression profiling was performed in comparison to splenic DCs. Transcriptome analysis of thymic APCs revealed differential expression of costimulatory molecules that could be involved in stable Treg generation. Importantly, both mTEC- and t-DC- induced alloantigen-specific Tregs displayed significantly higher efficacy in prolonging skin allograft acceptance when compared to alloantigen-specific Tregs generated by splenic DCs.
2017-03-15 | GSE67834 | GEO
Project description:dendritic cells = improtant APC -different subtypes characterized by surface markers by FACS -combination of FACS and LC-MS powerful tool, especially for low cell numbers -direct sorting of cells into SP3-compatible lysis buffer -new protocol without washing steps after sort and before protein digestion
2024-07-25 | PXD031960 | JPOST Repository
Project description:The presentation of self-antigens in the thymus by medullary thymic epithelial cells (mTECs) and dendritic cells (DCs) is crucial for the establishment of central tolerance. While mTECs produce and present self-antigens in an autonomous manner, DCs acquire them from mTECs by Cooperative Antigen Transfer (CAT). Although CAT represents a key process of central tolerance, molecular determinants which drive CAT are largely unknown. To reveal these determinants, we compared the transcriptomes of CAT-experienced and CAT-inexperienced DCs via scRNAseq. Specifically, we sequenced TdTOMATO+ and TdTOMATO– CD11c+ and CD11b+ cells from the thymus of Foxn1CreR26TdTOMATO mice. In this model, fluorescent TdTOMATO protein is exclusively produced by thymic epithelium, thus TdTOMATO expression in DCs (CD11c+ and CD11b+ cells) mark their previous experience of CAT. Using this approach we unraveled several candidate determinants of CAT. We focused on the gene determinant, Cldn1, encoding the tight junction protein Claudin 1, that was found to be highly expressed among the CAT-experienced type 1 lineage DCs. We performed further experiments that confirmed its role in driving CAT. In addition, this scRNAseq approach allowed us to redefine the heterogeneity and maturation states of thymic DCs.
2024-07-31 | E-MTAB-14319 | biostudies-arrayexpress
Project description:Dendritic cells (DCs) are professional antigen-presenting cells (APCs). The key functions of DCs include engulfing, processing and presenting antigens to T cells and regulating the activation of T cells. There are two major DC subtypes in human blood: plasmacytoid DCs (pDCs) and conventional DCs (cDCs). To define the differences between the adult and infant immune systems, especially in terms of DC constitution, we enriched dendritic cells from human cord blood and generated single-cell RNA sequencing data from ~7,000 cells using the 10X Genomics Single Cell 3’ Solution. After incorporating the differential expression analysis method in our clustering process, we identified all known dendritic cell subsets. Interestingly, we also found a group of DCs with gene expression that was a mix of megakaryocytes and pDCs. Further, we verified the expression of selected genes at both the RNA level by PCR and the protein level by flow cytometry. This study further demonstrates the power of single-cell RNA sequencing in dendritic cell research.
2019-12-03 | GSE141238 | GEO
Project description:Expression data from human Dendritic cells (DCs)
| PRJNA649123 | ENA
Project description:Among the dendritic cell (DC) subsets, plasmacytoid DCâs are thought to be important in both generating antiviral and antitumor responses. These cells may be useful in developing dendritic cell-based tumor vaccines, however, the rarity of these cells in the peripheral blood have hampered attempts to understand their biology. To provide better insight into the biology of plasmacytoid DCs, we isolated these cells from the peripheral blood of healthy donors in order to further characterize their gene expression. Using gene array technology we compared the genetic profiles of these cells to those of CD14+ monocytes isolated from the same donors and found several immune related genes upregulated in this cell population. Understanding the genetic profiles of this dendritic cell subtype as well as others such as the BDCA-1 expressing myeloid DCs may enable us to manipulate these cells ex-vivo to generate enhanced DC-based tumor vaccines inducing more robust antitumor responses. Experiment Overall Design: 4 replicates of BDCA cells and CD14 cells
2008-10-21 | E-GEOD-11943 | biostudies-arrayexpress
Project description:cDCs home from the periphery into the thymus. In order to determine the phenotypic and functional changes introduced by the thymic microenvironment to these thymus-homing cDCs, RNA-based next generation sequencing (RNAseq) was performed with splenic (sp-DC) and thymic conventional DCs (t-DCs) re-isolated from RTOCs after two days of culture. Methods: RTOCs were generated from single-cell suspensions of thymi isolated from E14.5 to E16.5 fetuses of Foxp3hCD2 reporter mice (BALB/c background), and sp‑DCs or t‑DCs sorted from 4-8 weeks old female CD45.1xBALB/c mice were introduced. After two days of culture, 1‑2x103 cDCs were re-isolated from RTOCs as CD45.1+Lin-CD11chi by FACS, and total RNA for transcriptional profiling by low-input RNAseq was isolated. Total RNA from sp-DC and t-DCs isolated ex vivo from 4-8 weeks old female CD45.1xBALB/c mice was used as control. RNAseq was performed on an Illumina HiSeq2500 system. Differential gene expression between the four different conditions was computed from the read counts. Results: The number of differentially expressed genes between ex vivo isolated sp-DC and t-DC was drastically reduced comparing sp-DCs and t-DCs re-isolated from RTOCs. This finding implies that the thymic microenvironment within an RTOC modulates the gene expression in sp‑DCs, conferring a transcriptomic profile that more closely resembled the one from t‑DCs. Conclusion: The thymic microenvironment modulates the transcriptome of thymus-homing peripheral cDCs.
2021-03-01 | GSE164280 | GEO
Project description:In this study transcriptome profiling of dendritic cell subtypes was performed using various human dendritic cells. Monocyte-derived DC: CD14+ monocytes were obtained from buffy coats by Ficoll - gradient centrifugation and immunomagnetic cell separation using anti-CD14-conjugated microbeads. Monocytes were resuspended into 6-well culture dishes at a density of 1.5 x 10 million cells/ml and cultured in RPMI 1640 supplemented with 10% FBS containing 800 U/ml GM-CSF and 500 U/ml IL-4. Cells were cultured for 5 days and the IL-4 and GM-CSF addition was repeated at day 2. Dermal DC (DDC) and Langerhans Cells (LC) from skin: Human skin specimens were obtained from healthy donors undergoing corrective breast or abdominal plastic surgery after informed consent. Thick slices (3 mm) of skin containing the epidermis and the dermis were cut by use of a dermatome. Slices of skin were cut in pieces of 1 cm2 and incubated with Dispase II for 30â60 min at 37°C. The epidermis and dermis were separated with tweezers and washed with PBS. To isolate LC, the epidermal sheets were incubated with PBS with 0.05% trypsin for 10 min at 37°C, and a single-cell suspension was prepared by pushing the tissue through 100 µm pore nylon cell strainers with a plunger of a 2-ml syringe. Epidermal cell suspension was enriched for LC by density centrifugation over Lymphoprep and CD1a-guided MACS (Miltenyi Biotec). To isolate DDC, the dermis was incubated with PBS containing Dispase and Collagenase A at 37°C for 2 h, after which, a single-cell suspension was prepared by pushing through 100 µm pore nylon cell strainers with a plunger of a 2-ml syringe. Cell suspension was enriched for DDC by CD1a-guided MACS. Blood Cd1c+ DC: Blood CD1c+ DC were isolated from periferal blood. BDCA1+ (CD1c) DCs were incubated with a lineage-specific PE-labeled Ab mixture, HLA-DR-allophycocyanin, and BDCA1-FITC. Lineage-negative and HLA-DRhigh DCs, positive for BDCA1 were sorted on a FACS and collected in tubes containing 1 ml of 100% FBS. A total of 40,000â100,000 cells was isolated (>98% pure). Dendritic cell subtypes were differentiated in vitro from monocytes and primary dendritic cells were isolated from human skin and blood.
2010-10-27 | E-GEOD-23618 | biostudies-arrayexpress