Bulk RNA sequencing of human mesenchymal stromal cells derived from labial salivary glands, bone marrow, and adipose
Data files
Nov 17, 2025 version files 12.57 MB
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gene_fpkm_dryad.txt
12.57 MB
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README.md
2.52 KB
Abstract
We obtained mesenchymal stromal cells from digested human tissue derived from bone marrow (n=3), adipose (n=3), and labial salivary glands (n=9). The salivary gland derived MSCs were from participants who met 2016 ACR/EULAR criteria for SjD (n=3), participants who had dry eye or dry mouth but no evidence of a systemic autoimmune disease (n=3), and participants who had no symptoms of dryness as controls (n=3). The samples were subjected to bulk RNA sequencing.
Dataset DOI: 10.5061/dryad.9ghx3ffv6
Description of the data and file structure
We collected tissue from bone marrow (n=3), omental adipose (n=3), or labial salivary gland tissue (n=9). The tissue was digested, and mesenchymal stromal cells were isolated, verified, and cryopreserved. The cells were sent to Novogene. They purified mRNA from total RNA with poly -T oligo attached magnetic beads and synthesized cDNA and generated a library. They checked the library with Qubit and rtPCR. the quantified library was pooled and sequenced using an Illumina platform. They followed their standard bioinformatics work flow that includes generation of raw data, data QC, mapping to reference genome, gene expression quantification, differential gene analysis, and functional analysis.
Also, we provide FASTQ files with nucleotide sequences and quality scores (forward and reverse) for each subject and treatment condition. Differentially expressed genes (DEGs) are included for multiple comparisons: markers_humanmsc_all lists DEGs for each cytokine treatment vs. all others; markers_ifng_vs_vehicle, markers_tnfa_vs_vehicle, and markers_it10_vs_vehicle compare DEGs for IFN-γ, TNF-α, and combined IFN-γ/TNF-α treatments versus vehicle, respectively and the data is available at: https://doi.org/10.5061/dryad.9ghx3ffv4
Files and variables
File: gene_fpkm_dryad.txt
Description:
Variables
- gene_id: ID of gene
- 1ns: 1st labial salivary gland MSC subject that did not have dryness (nonsicca control)
- 2ns: 2nd MSC from nonsicca control
- 3ns: 3rd MSC from nonsicca control
- 1siccact: 1st MSC from a sicca control (dryness but no autoimmunity)
- 2siccact: 2nd MSC from a sicca control
- 3siccact: 3rd MSC from a sicca control
- 1Sj: 1st MSC from a SjD patient
- 2Sj: 2nd MSC from a SjD patient
- 3Sj: 3rd MSC from a SjD patient
- 1BM: 1st bone marrow MSC
- 2BM: 2nd bone marrow MSC
- 3BM: 3rd bone marrow MSC
- 1Ad: 1st adipose MSC
- 2Ad: 2nd adipose MSC
- 3Ad: 3rd adipose MSC
- gene_name: gene symbol
- gene_chr: the chromosome of the gene
- gene_start: the start site of the gene
- gene_end: the end site of the gene
- gene_strand: the direction of the gene chain
- gene_length: the length of the gene
- gene_biotype: the biotype of gene
- gene_description: the description of gene
- tf_family: the transcription factor of gene