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Sample GSM5461603 Query DataSets for GSM5461603
Status Public on Aug 04, 2021
Title 1321: Primary Human MSCs - #5 donor - untreated
Sample type SRA
Source name Mesenchymal Stromal Cells
Organism Homo sapiens
Characteristics cells: primary MSCs (Mesenchymal Stromal Cells)
tissue: bone marrow-derived
treatment: untreated/control
donor sex: male
donor age: 39
Treatment protocol Two methods of hypoxic preconditioning were used. The first, "physical" hypoxia was achieved by culturing cells for 6h in a gas mixture composed of 2% O2 (balanced with N2) and 5% CO2. The second, "pharmacological" hypoxia was obtained by culturing cells for 6h with the PHDs inhibitor, Vadadustat (AKB-6548, Akebia, Cambridge, MA, USA) in a concentration of 40 μM. Vadadustat was prepared as a 5 mM stock solution in DMSO according to the manufacturer's instructions, meaning that no more than 0.8 % (v/v) DMSO was present in the culture medium. After 6 h of incubation, cells were harvested, washed with PBS and frozen at -80°C for further analysis.
Growth protocol Routine MSCs cultures were maintained under conditions of 5% CO2, 95% humidified air at 37°C. For the analyses, we used six BM-MSCs populations that were between passage 4 and 6 and that fulfilled acknowledged identification criteria for MSCs.
Extracted molecule total RNA
Extraction protocol The incubation lasted for 6 h, after which we removed the medium from the cell cultures, washed cells with PBS and disrupted them by scraping in 350 μL of RLT isolation buffer from Qiagen RNeasy Mini Kit according to the protocol provided by the manufacturer.
cDNA libraries construction was carried out with 1μg of total RNA using TruSeq Stranded mRNA Library Prep Kit ( Illumina, San Diego, CA, USA) according to the manufacturer’s instruction.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1500
Description *** Raw data not submitted due to patient privacy concerns (currently under IRB review) ***
Data processing Basecalls performed using CASAVA version 1.7
Paired-end sequencing (2x100 bp) performed using the HiSeq1500 platform with an average of 16 - 20 million read pairs generated for each library.
Quality control checks of the sequencing raw data conducted with FastQC, and adapter-trimming with BBDUK2 tool.
Quantification of transcript abundance and gene expression was performed using Salmon software.
Exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: tab-delimited text files include raw gene counts for each sample.
Supplementary_files_format_and_content: Matrix table with normalized gene counts generated by DESeq2 used for GSEA analysis
Submission date Jul 19, 2021
Last update date Aug 04, 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
Platform ID GPL18460
Series (1)
GSE180371 Gene expression profile of human mesenchymal stromal cells (MSCs) exposed to hypoxic and pseudohypoxic preconditioning
BioSample SAMN20306345

Supplementary file Size Download File type/resource
GSM5461603_1321.sf.gz 2.0 Mb (ftp)(http) SF
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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