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Series GSE180371 Query DataSets for GSE180371
Status Public on Aug 04, 2021
Title Gene expression profile of human mesenchymal stromal cells (MSCs) exposed to hypoxic and pseudohypoxic preconditioning
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary We performed gene expression profiling by RNA sequencing (RNA-Seq) to fully characterize the gene regulation effect induced by exposure of MSCs to two hypoxic preconditioning methods. We determined the gene expression profile of 6 populations of human MSCs isolated from bone marrow and preconditioned for 6h in 2% O2 (hypoxia) or with 40μM Vadadustat (pseudohypoxia), compared to control cells cultured in 21% O2. There were 5 populations isolated from males and 1 population isolated from a female. The mean age of the BM-MSCs donors was 50.5 years and the median was 44 years. RNA-Sequencing was performed using the Illumina platform. For each library an average of 16 - 20 million read pairs were generated. Quality control checks of the sequencing raw data was conducted with FastQC, while adapter-trimming was performed with BBDUK2. The relative expression of transcripts were quantified for each donor using the Salmon program v0.8.1. Fastq files were mapped to the Homo_sapiens.GRCh37 reference genome using HISAT2 software version 2.1.0. The tximport pipeline was used to import transcript abundance datasets for the differential gene expression analysis for three groups: Control vs. Vadadustat, Control vs. Hypoxia and Vadadustat vs. Hypoxia by DESeq2 software version 1.14.1. Our results provide insight into the transcriptomic effects of these two methods of hypoxic preconditioning of MSCs.
Overall design mRNA profiles of human MSCs preconditioned in hypoxia and with Vadadustat
*** Raw data not submitted due to patient privacy concerns (currently under IRB review) ***
Contributor(s) Zielniok K, Burdzinska A, Murcia Pienkowski V, Koppolu A, Rydzanicz M, Zagozdzon R, Paczek L
Citation(s) 34360925
Submission date Jul 19, 2021
Last update date Sep 05, 2021
Contact name Katarzyna Zielniok
Organization name Medical University of Warsaw
Department Department of Clinical Immunology
Lab Laboratory of Cellular and Genetic Therapies
Street address Nowogrodzka 59
City Warsaw
ZIP/Postal code 02-006
Country Poland
Platforms (1)
GPL18460 Illumina HiSeq 1500 (Homo sapiens)
Samples (18)
GSM5461591 1309: Primary Human MSCs - #1 donor - untreated
GSM5461592 1310: Primary Human MSCs - #1 donor - preconditioned in hypoxia
GSM5461593 1311: Primary Human MSCs - #1 donor - preconditioned with Vadadustat
BioProject PRJNA748022

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE180371_Normalized_gene_counts_matrix.txt.gz 602.8 Kb (ftp)(http) TXT
GSE180371_RAW.tar 36.2 Mb (http)(custom) TAR (of SF)
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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