Single-cell RNA sequencing of human salivary gland derived mesenchymal stromal cells under cytokine treatment conditions
Data files
Nov 17, 2025 version files 107.56 GB
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30220_R1_001.fastq.gz
4.48 GB
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30220_R2_001.fastq.gz
3.77 GB
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30221_R1_001.fastq.gz
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30221_R2_001.fastq.gz
3.13 GB
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30222_R1_001.fastq.gz
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30222_R2_001.fastq.gz
2.13 GB
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30223_R1_001.fastq.gz
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30223_R2_001.fastq.gz
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30224_R1_001.fastq.gz
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30224_R2_001.fastq.gz
1.78 GB
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30225_R1_001.fastq.gz
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30225_R2_001.fastq.gz
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30226_R1_001.fastq.gz
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30226_R2_001.fastq.gz
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30227_R1_001.fastq.gz
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30227_R2_001.fastq.gz
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30228_R1_001.fastq.gz
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30228_R2_001.fastq.gz
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30229_R1_001.fastq.gz
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30229_R2_001.fastq.gz
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30230_R1_001.fastq.gz
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30230_R2_001.fastq.gz
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30231_R1_001.fastq.gz
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30231_R2_001.fastq.gz
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markers_humanmsc_all.csv
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markers_IFNg_vs_vehicle.csv
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markers_IT10_vs_vehicle.csv
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markers_TNFa_vs_vehicle.csv
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README.md
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Abstract
Mesenchymal stromal cells (MSCs) reside in tissue stroma and are associated with potent immunomodulatory and trophic properties. Furthermore, the immunomodulatory properties of MSCs are traditionally optimized with cytokine stimulation such as with IFNγ or both IFNγ and TNFα. The effect of these cytokines on MSC(SG) are unknown. We report the study of labial salivary gland-derived MSCs (MSC[SG]) as a potential MSC source with beneficial immunomodulatory and trophic properties. We studied MSC(SG) after cytokine pre-licensing with vehicle, IFNγ, TNFα, or both IFNγ and TNFα (dual treatment).
Dataset DOI: 10.5061/dryad.9ghx3ffv4
Description of the data and file structure
Single-cell RNA sequencing of salivary gland-derived mesenchymal stromal cells treated with cytokines
Methods
Labial salivary gland-derived mesenchymal stromal cells from human participants. The cells were isolated, expanded, and treated with the following conditions: 1) vehicle; 2) 60 ng/mL IFN-gamma; 3) 10 ng/mL TNF-alpha; 4) both 60 ng/mL IFN-gamma and 10 ng/mL TNF-alpha. Treatment occurred for 24 hours before cryopreservation.
Description of the data and file structure
We include fastq files for nucleotide sequence information along with quality scores for each sequenced nucleotide in forward and reverse for each treatment condition and each subject.
We include DEGs in several comparisons. markers_humanmsc_all includes a table with the DEGs in each cytokine treatment condition vs. all others. markers_ifng_vs_vehicle compares DEGs between IFN-gamma treated MSCs to vehicle. markers_TFNa_vs_vehicle compares DEGs between TNF-alpha treated MSCs to vehicle. markers_IT10_vs_vehicle compares DEGs between the combined IFN-gamma and TNF-alpha treated MSCs to vehicle.
These reads originate from human samples, but they do not contain any genetic variant information.
Also, tissue was collected from bone marrow (n=3), omental adipose (n=3), and labial salivary gland (n=9). Samples were digested to isolate mesenchymal stromal cells, which were verified, cryopreserved, and sent to Novogene. mRNA was purified from total RNA using poly-T oligo magnetic beads, converted to cDNA, and used to generate sequencing libraries. Libraries were quality-checked with Qubit and qPCR, pooled, and sequenced on an Illumina platform. Standard bioinformatics workflows were applied, including raw data generation, QC, mapping to the reference genome, gene expression quantification, differential expression analysis, and functional annotation and the data is available at: https://doi.org/10.5061/dryad.9ghx3ffv6
Files and variables
File: markers_humanmsc_all.csv
Description: markers_ifng_vs_vehicle compares DEGs between IFN-gamma treated MSCs to vehicle.
Variables
- p_val: the p value
- avg_log2FC: the average log 2 fold change
- pct.1: percentage of expression group 1
- pct.2: percentage of expression in group 2
- p_val_adj: adjusted p-value
- cluster: description of treatments
- gene: the gene for which data are presented in the row
File: markers_IFNg_vs_vehicle.csv
Description:
Variables
- gene: the gene for which data are presented in the row
- p_val: the p value
- avg_log2FC: the average log 2 fold change
- pct.1: percentage of expression group 1
- pct.2: percentage of expression in group 2
- p_val_adj: adjusted p-value
File: markers_IT10_vs_vehicle.csv
Description: treatment with both interferon and TNF-alpha vs. vehicle
Variables
- gene: the gene for which data are presented in the row
- p_val: the p value
- avg_log2FC:
- pct.1:
- pct.2:
- p_val_adj:
File: markers_TNFa_vs_vehicle.csv
Description: treatment with TNF-alpha vs. vehicle
Variables
- gene: the gene for which data are presented in the row
- p_val: the p value
- avg_log2FC:
- pct.1:
- pct.2:
- p_val_adj:
File: 30220_R1_001
Description: Vehicle treated fastq files for cell line from subject 1. Forward Reads.
Variables
- Read identifier
- Nucleotide sequence
- Separator Line
- Quality score (ASCII-encoded Phred scores)
File: 30220_R2_001
Description: Vehicle treated fastq files for cell line from subject 1. Reverse Reads.
Variables
- Read identifier
- Nucleotide sequence
- Separator Line
- Quality score (ASCII-encoded Phred scores)
File: 30221_R1_001
Description: Interferon-gamma and TNF-alpha treated fastq files for cell line from subject 1. Forward Reads.
Variables
- Read identifier
- Nucleotide sequence
- Separator Line
- Quality score (ASCII-encoded Phred scores)
File: 30221_R2_001
Description: Interferon-gamma and TNF-alpha treated fastq files for cell line from subject 1. Reverse Reads.
Variables
- Read identifier
- Nucleotide sequence
- Separator Line
- Quality score (ASCII-encoded Phred scores)
File: 30222_R1_001
Description: TNF-alpha treated fastq files for cell line from subject 1. Forward Reads.
Variables
- Read identifier
- Nucleotide sequence
- Separator Line
- Quality score (ASCII-encoded Phred scores)
File: 30222_R2_001
Description: TNF-alpha treated fastq files for cell line from subject 1. Reverse Reads.
Variables
- Read identifier
- Nucleotide sequence
- Separator Line
- Quality score (ASCII-encoded Phred scores)
File: 30223_R1_001
Description: Interferon-gamma treated fastq files for cell line from subject 1. Forward Reads.
Variables
- Read identifier
- Nucleotide sequence
- Separator Line
- Quality score (ASCII-encoded Phred scores)
File: 30223_R2_001
Description: Interferon-gamma and TNF-alpha treated fastq files for cell line from subject 1. Reverse Reads.
Variables
- Read identifier
- Nucleotide sequence
- Separator Line
- Quality score (ASCII-encoded Phred scores)
File: 30224_R1_001
Description: Vehicle treated fastq files for cell line from subject 2. Forward Reads.
Variables
- Read identifier
- Nucleotide sequence
- Separator Line
- Quality score (ASCII-encoded Phred scores)
File: 30224_R2_001
Description: Vehicle treated fastq files for cell line from subject 2. Reverse Reads.
Variables
- Read identifier
- Nucleotide sequence
- Separator Line
- Quality score (ASCII-encoded Phred scores)
File: 30225_R1_001
Description: Interferon-gamma and TNF-alpha treated fastq files for cell line from subject 2. Forward Reads.
Variables
- Read identifier
- Nucleotide sequence
- Separator Line
- Quality score (ASCII-encoded Phred scores)
File: 30225_R2_001
Description: Interferon-gamma and TNF-alpha treated fastq files for cell line from subject 2. Reverse Reads.
Variables
- Read identifier
- Nucleotide sequence
- Separator Line
- Quality score (ASCII-encoded Phred scores)
File: 30226_R1_001
Description: TNF-alpha treated fastq files for cell line from subject 2. Forward Reads.
Variables
- Read identifier
- Nucleotide sequence
- Separator Line
- Quality score (ASCII-encoded Phred scores)
File: 30226_R2_001
Description: TNF-alpha treated fastq files for cell line from subject 2. Reverse Reads.
Variables
- Read identifier
- Nucleotide sequence
- Separator Line
- Quality score (ASCII-encoded Phred scores)
File: 30227_R1_001
Description: Interferon-gamma treated fastq files for cell line from subject 2. Forward Reads.
Variables
- Read identifier
- Nucleotide sequence
- Separator Line
- Quality score (ASCII-encoded Phred scores)
File: 30227_R2_001
Description: Interferon-gamma and TNF-alpha treated fastq files for cell line from subject 2. Reverse Reads.
Variables
- Read identifier
- Nucleotide sequence
- Separator Line
- Quality score (ASCII-encoded Phred scores)
File: 30228_R1_001
Description: Vehicle treated fastq files for cell line from subject 3. Forward Reads.
Variables
- Read identifier
- Nucleotide sequence
- Separator Line
- Quality score (ASCII-encoded Phred scores)
File: 30228_R2_001
Description: Vehicle treated fastq files for cell line from subject 3. Reverse Reads.
Variables
- Read identifier
- Nucleotide sequence
- Separator Line
- Quality score (ASCII-encoded Phred scores)
File: 30229_R1_001
Description: Interferon-gamma and TNF-alpha treated fastq files for cell line from subject 3. Forward Reads.
Variables
- Read identifier
- Nucleotide sequence
- Separator Line
- Quality score (ASCII-encoded Phred scores)
File: 30229_R2_001
Description: Interferon-gamma and TNF-alpha treated fastq files for cell line from subject 3. Reverse Reads.
Variables
- Read identifier
- Nucleotide sequence
- Separator Line
- Quality score (ASCII-encoded Phred scores)
File: 30230_R1_001
Description: TNF-alpha treated fastq files for cell line from subject 3. Forward Reads.
Variables
- Read identifier
- Nucleotide sequence
- Separator Line
- Quality score (ASCII-encoded Phred scores)
File: 30230_R2_001
Description: TNF-alpha treated fastq files for cell line from subject 3. Reverse Reads.
Variables
- Read identifier
- Nucleotide sequence
- Separator Line
- Quality score (ASCII-encoded Phred scores)
File: 30231_R1_001
Description: Interferon-gamma treated fastq files for cell line from subject 3. Forward Reads.
Variables
- Read identifier
- Nucleotide sequence
- Separator Line
- Quality score (ASCII-encoded Phred scores)
File: 30231_R2_001
Description: Interferon-gamma and TNF-alpha treated fastq files for cell line from subject 3. Reverse Reads.
Variables
- Read identifier
- Nucleotide sequence
- Separator Line
- Quality score (ASCII-encoded Phred scores)
Mesenchymal stromal cells were isolated from three biologically distinct human labial salivary glands.Patients were healthy controls who had head and neck cancer that did not involve the labial salivary gland and did not have any dryness symptoms. After expansion to 80% confluence, each of the three biologiacal replicates were treated with vehicle, 60 ng/mL of IFNγ and 10 ng/mL of TNFα for 24 hours.