Single-cell transcriptomics uncovers human corneal limbal stem cells and its differentiation trajectory

Experiment ID:SRP269263
Technology:scRNA-Seq
Description:Limbal stem cells (LSCs), known as corneal epithelial stem cells, are located at the basal epithelial layer of the corneal limbus and serve an important function in maintaining the homeostasis of the corneal epithelium. Several putative molecular markers of LSCs have been previously identified. However, the specificity of these markers remains largely controversial. To address this gap in the current understanding of LSCs, we performed a transcriptome profiling of heterogeneous corneal limbal basal cells using single-cell transcriptomics technology to identify LSCs and their exclusive markers. We isolated limbal basal cells from two young donors, constructed scRNA-seq libraries, generated RNA-sequencing data using the 10x Genomics platform, and then finally obtained the transcriptome of about 18,000 individual single-cells using Cell ranger (https://10xgenomics.com). Next, we performed quality control, filtering and data integration using Seurat package (https://satijalab.org/seurat), about 16,400 cells were retained for further downstream analysis such as dimensional reduction, unsupervised clustering, and Differentially expressed gene selection, trajectory analysis and visualization. We identified 11 unique clusters of cells assigned to a putative cell type based on published known biomarkers for differentiation, proliferation and putative epithelial stem cells. As a results, we found 2 Terminally Differentiated Cell (TDC), 3 Post-Mitotic Cell (PMC), 1 Transient Amplifying Cell (TAC), 2 Limbal Progenitor Cell (LPC), Putative Limbal Stem Cell (LSC) and 2 Melanocyte (MC) sub-cell type clusters. Furthermore, we confirmed the trajectory order of LSC differentiation for 9 clusters using Pseudotemporal and Functional PCA analysis. Lastly, we validated each assigned cell subtypes and determined their location in human corneal limbus tissue with 9 markers using RNAscope We were able to reveal the heterogeneity of corneal limbal basal epithelium by defining novel dynamic trajectories for cell types in a pseudotemporal manner. This approach allowed us to identify the distinct clusters of LSCs and progenitors with exclusively expressed markers, and might apply for translational research on regenerating a normal corneal epithelium and restoring vision. Overall design: We isolated limbal basal cells from two young donors, constructed scRNA-seq libraries, generated RNA-sequencing data using the 10x Genomics platform, and then finally obtained the transcriptome of about 18,000 individual single-cells using Cell ranger (https://10xgenomics.com). Next, we performed quality control, filtering and data integration and further downstream analysis such as dimensional reduction, unsupervised clustering, and Differentially expressed gene selection, trajectory analysis and visualization.
DOI:10.1016/j.jtos.2020.12.004
Source:SRP269263 SRA
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scRNA-Seq droplet-based processed expression values per cell population in Homo sapiensscRNA-Seq droplet-based H5AD data per cell in Homo sapiens

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Library ID
Identifier of the RNA-Seq library
Cell type ID
ID of the cell type of the sample
Cell type name
Name of the cell type of the sample
Cell type author annotation
Free text annotation of cell type as provided by authors
Anat. entity ID
ID of the anatomical localization of the sample
Anat. entity name
Name of the anatomical localization of the sample
Anat. entity author annotation
Free text annotation of anatomical localization of the sample as provided by authors
Stage ID
ID of the developmental and life stage of the sample
Stage name
Name of the developmental and life stage of the sample
Stage author annotation
Free text annotation of the developmental and life stage of the sample as provided by authors
Sex
Annotation of the sex of the sample
Strain
Annotation of the strain of the sample
Time
Free text annotation of the time of sampling as provided by authors
Time unit
Unit for the time of sampling as provided by authors
Species
Physiological status
Physiological status of the organism at time of sampling
Technology
Sequencing platform
Sequenced transcript part
Possible values are: full length, all parts of the transcript are sequenced; 3': only the 3' end of the transcript is sequenced; 5': only the 5' end of the transcript is sequenced.
Fractionation
Possible values are: cell, transcripts are extracted from the cell; nuclei, transcripts are extracted from the nucleus.
Fragmentation
Size of the RNA fragmentation
Run sequencing type
Paired-end or single-read run
Total read count
Total number of reads for the library.
Mapped read count
Number of reads that could be mapped to the transcriptome.
Total UMI count
Total number of individual RNA molecules (UMI) for the annotated sample. Only applicable for libraries producing UMIs.
Mapped UMI count
Number of UMIs that could be mapped to the transcriptome. Only applicable for libraries producing UMIs.
Distinct rank count
When performing a fractional ranking of the genes in the annotated sample, based on their expression level, number of distinct ranks observed, to have a value of the power for distinguishing expression levels. Used as a weight to compute a weighted mean rank accross samples for each gene and compute expression scores in Bgee.
Max rank
When performing a fractional ranking of the genes in the annotated sample, based on their expression level, maximum rank attained in the sample. Used to normalize ranks accross samples and compute expression scores in Bgee.
Link to processed expression values
See the processed expression value results for this assay
SRX8635112CL:0000575 corneal epithelial cellTDC (terminally differentiated cells)UBERON:0006761 corneo-scleral junctioncorneal limbal epithelial basal layerHsapDv:0000237 third decade stage (human)young donors (adut in HCA)NANANANAHomo sapiensNA10X Genomics V2Illumina NovaSeq 6000THREE_PRIMECELL0paired823020840543260720035131569702027969Browse results
SRX8635112CL:0011026 progenitor cellLPC (Limbal Progenitor Cell)UBERON:0006761 corneo-scleral junctioncorneal limbal epithelial basal layerHsapDv:0000237 third decade stage (human)young donors (adut in HCA)NANANANAHomo sapiensNA10X Genomics V2Illumina NovaSeq 6000THREE_PRIMECELL0paired823020840543260720011816266426227148Browse results
SRX8635112CL:0000055 non-terminally differentiated cellPMC (Post-Mitotic Cell)UBERON:0006761 corneo-scleral junctioncorneal limbal epithelial basal layerHsapDv:0000237 third decade stage (human)young donors (adut in HCA)NANANANAHomo sapiensNA10X Genomics V2Illumina NovaSeq 6000THREE_PRIMECELL0paired823020840543260720033149352691927932.5Browse results
SRX8635112CL:0009010 transit amplifying cellTAC (Transient Amplifying Cell)UBERON:0006761 corneo-scleral junctioncorneal limbal epithelial basal layerHsapDv:0000237 third decade stage (human)young donors (adut in HCA)NANANANAHomo sapiensNA10X Genomics V2Illumina NovaSeq 6000THREE_PRIMECELL0paired82302084054326072004932472355326233Browse results
SRX8635112CL:0000034 stem cellLSC (Limbal Stem Cell)UBERON:0006761 corneo-scleral junctioncorneal limbal epithelial basal layerHsapDv:0000237 third decade stage (human)young donors (adut in HCA)NANANANAHomo sapiensNA10X Genomics V2Illumina NovaSeq 6000THREE_PRIMECELL0paired8230208405432607200601333101824266Browse results
SRX8635113CL:0000575 corneal epithelial cellTDC (terminally differentiated cells)UBERON:0006761 corneo-scleral junctioncorneal limbal epithelial basal layerHsapDv:0000237 third decade stage (human)young donors (adut in HCA)NANANANAHomo sapiensNA10X Genomics V2Illumina NovaSeq 6000THREE_PRIMECELL0paired861610927543214753035400964630727706.5Browse results
SRX8635113CL:0011026 progenitor cellLPC (Limbal Progenitor Cell)UBERON:0006761 corneo-scleral junctioncorneal limbal epithelial basal layerHsapDv:0000237 third decade stage (human)young donors (adut in HCA)NANANANAHomo sapiensNA10X Genomics V2Illumina NovaSeq 6000THREE_PRIMECELL0paired861610927543214753020294873460727328.5Browse results
SRX8635113CL:0000055 non-terminally differentiated cellPMC (Post-Mitotic Cell)UBERON:0006761 corneo-scleral junctioncorneal limbal epithelial basal layerHsapDv:0000237 third decade stage (human)young donors (adut in HCA)NANANANAHomo sapiensNA10X Genomics V2Illumina NovaSeq 6000THREE_PRIMECELL0paired861610927543214753054474143696628225Browse results
SRX8635113CL:0009010 transit amplifying cellTAC (Transient Amplifying Cell)UBERON:0006761 corneo-scleral junctioncorneal limbal epithelial basal layerHsapDv:0000237 third decade stage (human)young donors (adut in HCA)NANANANAHomo sapiensNA10X Genomics V2Illumina NovaSeq 6000THREE_PRIMECELL0paired86161092754321475305535487292526159Browse results
SRX8635113CL:0000034 stem cellLSC (Limbal Stem Cell)UBERON:0006761 corneo-scleral junctioncorneal limbal epithelial basal layerHsapDv:0000237 third decade stage (human)young donors (adut in HCA)NANANANAHomo sapiensNA10X Genomics V2Illumina NovaSeq 6000THREE_PRIMECELL0paired86161092754321475308520330921462Browse results

Showing 1 to 10 of 10 entries

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