DOI: 10.5061/dryad.9ghx3ffv4
title: Single-cell RNA sequencing of human salivary gland derived mesenchymal stromal cells under cytokine treatment conditions

description: 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). 
description: 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. 
description: # Single-cell RNA sequencing of human salivary gland derived mesenchymal
 stromal cells under cytokine treatment conditions Dataset DOI:
 [10.5061/dryad.9ghx3ffv4](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 1. Read
 identifier 2. Nucleotide sequence 3. Separator Line 4. Quality score
 (ASCII-encoded Phred scores) #### File: 30220_R2_001 **Description:** 
 Vehicle treated fastq files for cell line from subject 1. Reverse Reads. 
 ##### Variables 1. Read identifier 2. Nucleotide sequence 3. Separator
 Line 4. 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 1. Read
 identifier 2. Nucleotide sequence 3. Separator Line 4. 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 1. Read identifier 2.
 Nucleotide sequence 3. Separator Line 4. 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
 1. Read identifier 2. Nucleotide sequence 3. Separator Line 4. 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 1. Read identifier 2. Nucleotide
 sequence 3. Separator Line 4. 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 1.
 Read identifier 2. Nucleotide sequence 3. Separator Line 4. 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 1. Read identifier 2.
 Nucleotide sequence 3. Separator Line 4. Quality score (ASCII-encoded
 Phred scores) #### File: 30224_R1_001 **Description:**  Vehicle treated
 fastq files for cell line from subject 2. Forward Reads.  ##### Variables
 1. Read identifier 2. Nucleotide sequence 3. Separator Line 4. Quality
 score (ASCII-encoded Phred scores) #### File: 30224_R2_001
 **Description:**  Vehicle treated fastq files for cell line from subject
 2. Reverse Reads.  ##### Variables 1. Read identifier 2. Nucleotide
 sequence 3. Separator Line 4. 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 1. Read identifier 2. Nucleotide sequence 3. Separator Line 4.
 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 1. Read
 identifier 2. Nucleotide sequence 3. Separator Line 4. 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 1. Read identifier 2. Nucleotide sequence 3.
 Separator Line 4. 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 1. Read identifier 2.
 Nucleotide sequence 3. Separator Line 4. 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 1. Read identifier 2. Nucleotide sequence 3. Separator Line 4.
 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 1. Read
 identifier 2. Nucleotide sequence 3. Separator Line 4. Quality score
 (ASCII-encoded Phred scores) #### File: 30228_R1_001 **Description:** 
 Vehicle treated fastq files for cell line from subject 3. Forward Reads. 
 ##### Variables 1. Read identifier 2. Nucleotide sequence 3. Separator
 Line 4. Quality score (ASCII-encoded Phred scores) #### File: 30228_R2_001
 **Description:**  Vehicle treated fastq files for cell line from subject
 3. Reverse Reads.  ##### Variables 1. Read identifier 2. Nucleotide
 sequence 3. Separator Line 4. 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 1. Read identifier 2. Nucleotide sequence 3. Separator Line 4.
 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 1. Read
 identifier 2. Nucleotide sequence 3. Separator Line 4. 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 1. Read identifier 2. Nucleotide sequence 3.
 Separator Line 4. 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 1. Read identifier 2.
 Nucleotide sequence 3. Separator Line 4. 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 1. Read identifier 2. Nucleotide sequence 3. Separator Line 4.
 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 1. Read
 identifier 2. Nucleotide sequence 3. Separator Line 4. Quality score
 (ASCII-encoded Phred scores)