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| 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
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| 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.
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| 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) ***
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| 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
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| Lab |
Laboratory of Cellular and Genetic Therapies
|
| Street address |
Nowogrodzka 59
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| City |
Warsaw |
| ZIP/Postal code |
02-006 |
| Country |
Poland |
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| Platforms (1) |
| GPL18460 |
Illumina HiSeq 1500 (Homo sapiens) |
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| Samples (18)
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| 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 |
| GSM5461594 |
1312: Primary Human MSCs - #2 donor - untreated |
| GSM5461595 |
1313: Primary Human MSCs - #2 donor - preconditioned in hypoxia |
| GSM5461596 |
1314: Primary Human MSCs - #2 donor - preconditioned with Vadadustat |
| GSM5461597 |
1315: Primary Human MSCs - #3 donor - untreated |
| GSM5461598 |
1316: Primary Human MSCs - #3 donor - preconditioned in hypoxia |
| GSM5461599 |
1317: Primary Human MSCs - #3 donor - preconditioned with Vadadustat |
| GSM5461600 |
1318: Primary Human MSCs - #4 donor - untreated |
| GSM5461601 |
1319: Primary Human MSCs - #4 donor - preconditioned in hypoxia |
| GSM5461602 |
1320: Primary Human MSCs - #4 donor - preconditioned with Vadadustat |
| GSM5461603 |
1321: Primary Human MSCs - #5 donor - untreated |
| GSM5461604 |
1322: Primary Human MSCs - #5 donor - preconditioned in hypoxia |
| GSM5461605 |
1323: Primary Human MSCs - #5 donor - preconditioned with Vadadustat |
| GSM5461606 |
1324: Primary Human MSCs - #6 donor - untreated |
| GSM5461607 |
1325: Primary Human MSCs - #6 donor - preconditioned in hypoxia |
| GSM5461608 |
1326: Primary Human MSCs - #6 donor - preconditioned with Vadadustat |
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| Relations |
| BioProject |
PRJNA748022 |
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