PRJNA506660: Single cell profiling of CD4+ T cells from human fetal intestine
Summary: The fetus is thought to be protected from exposure to foreign antigens, yet CD45RO+ T-cells reside in the fetal intestine. We combined functional assays with mass cytometry, single-cell RNA-sequencing, and high-throughput TCR-sequencing to characterize the fetal intestinal CD4+ T-cell compartment. We identified 22 CD4+ T-cell clusters, including naive-like, regulatory-like, and memory-like subpopulations, which were confirmed and further characterized at the transcriptional level. Memory-like cells expressed high levels of Ki-67, indicating cell division, and CD5, a surrogate marker of TCR-avidity, and produced IFN-γ and IL-2. Pathway analysis revealed a differentiation trajectory associated with cellular activation and proinflammatory effector functions, and TCR-repertoire analysis demonstrated clonal expansions, distinct repertoire characteristics, and interconnections between subpopulations of memory-like CD4+ T-cells. Imaging-mass cytometry further showed that memory-like CD4+ T-cells colocalized with antigen-presenting cells. Collectively, these results provided evidence for the generation of memory-like CD4+ T-cells in the human fetal intestine, consistent with exposure to foreign antigens.
Overall Design: Single, live, CD3+CD8a–TCRγδ–CD4+/– T-cells from one human fetal intestines were processed on the Chromium 3' single cell platform (10x Genomics) and sequenced on an Illumina HiSeq 4000.
| Strategy: |
|
| Species: |
|
| Tissue: |
|
| Healthy Condition: |
|
| Cell Type: |
|
| Growth Protocol: |
- |
| Treatment Protocol: |
Single, live, CD3+CD8a–TCRγδ–CD4+/–T-cells from the intestines of fetus #6 were sorted using a FACSAria III flow cytometer (BD Biosciences). Post-sort purity was 96.5%. |
| Extract Protocol: |
A single-cell suspension was prepared following the 10X Genomics single cell sample preparation protocol. |
| Library Construction Protocol: |
Droplet-based single-cell partitioning and single-cell RNA-Seq libraries were generated using the Chromium Single-Cell 3'Reagent v2 Kit (10X Genomics, Pleasanton, CA) as per the manufacturer' protocol. |
| Molecule Type: |
poly(A)+ RNA |
| Library Source: |
|
| Library Layout: |
PAIRED |
| Library Strand: |
Forward |
| Platform: |
ILLUMINA |
| Instrument Model: |
Illumina HiSeq 4000 |
| Strand-Specific: |
Specific |
| Data Resource |
GEN Sample ID |
GEN Dataset ID |
Project ID |
BioProject ID |
Sample ID |
Sample Name |
BioSample ID |
Sample Accession |
Experiment Accession |
Release Date |
Submission Date |
Update Date |
Species |
Race |
Ethnicity |
Age |
Age Unit |
Gender |
Source Name |
Tissue |
Cell Type |
Cell Subtype |
Cell Line |
Disease |
Disease State |
Development Stage |
Mutation |
Phenotype |
Case Detail |
Control Detail |
Growth Protocol |
Treatment Protocol |
Extract Protocol |
Library Construction Protocol |
Molecule Type |
Library Layout |
Strand-Specific |
Library Strand |
Spike-In |
Strategy |
Platform |
Instrument Model |
Cell Number |
Reads Number |
Gbases |
AvgSpotLen1 |
AvgSpotLen2 |
Uniq Mapping Rate |
Multiple Mapping Rate |
Coverage Rate |
Memory CD4+ T cells are generated in the human fetal intestine.
Nature immunology . 2019-01-21 [PMID:
30664737]
