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Sample GSM4128690 Query DataSets for GSM4128690
Status Public on Nov 01, 2019
Title Bone marrow stromal cells, S1209
Sample type SRA
 
Source name bone marrow stromal cells
Organism Homo sapiens
Characteristics donor: BM374
gender: M
age: 68
diabetes: h
passage: P4
stimulation: STIM
cell type: bone marrow-derived stromal cells (BMSC)
Treatment protocol A subset of n = 7 donors was treated for 24 h with or without cytokines (TNF-alpha and IFN-gamma, both 10 ng/mL), which werematched to the corresponding unstimulated cells and processed in parallel.
Growth protocol The cells were isolated from metaphyseal bone marrow (BM) biopsies from patients undergoing hip replacement at Charité University Hospital. Briefly, the BM mononuclear cell fraction (BM-MNC) in primary BM and the BMSC fraction post Ficoll-density gradient centrifugation (Histopaque 1077; Sigma-Aldrich) were quantified with an automated electrical impedance-based CASYR Cell Counter (Schaerfe System GmbH). The BMSCcontaining interphase was plated in a 300 cm2 tissue culture flask (ThermoFischer) and cultured under standard conditions (37◦C, 5% CO2) in an expansion medium (Dulbecco’s Modified Eagle Medium-Low Glucose [DMEM-LG; Sigma-Aldrich] containing 10% fetal calf serum [FCS; Biochrom AG], 100 U/mL penicillin, and 100μg/mL streptomycin [Biochrom AG], and 2mM L-alanyl-L-glutamine [GlutaMAX; Gibco]). The non-adherent fraction was removed by washing with PBS (Gibco), the medium was changed every 72 h, and the cells were allowed to reach about 80% confluence before passaging. The BMSCs were then expanded for several passages and were characterized with multiple functional and molecular assays, in line with the minimal criteria of the International Society for Cellular Therapy (ISCT) (69), at passage three (P3, early passage) and six (P6, late passage).
Extracted molecule polyA RNA
Extraction protocol Total RNA was extracted by using the Qiagen RNeasy Plus Mini Kit (Qiagen), according to the manufacturer’s instructions.
Poly-(A)-selection was performed utilizing the NEBNext Poly(A)mRNA Magnetic Isolation Module (NEB) according to the manufacturers requirements. mRNA libraries were prepared with the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB). All libraries were analyzed with the Agilent DNA 1000 Kit and quantified using the Qubit® dsDNA BR Assay Kit (ThermoFisher). After equimolar pooling all samples were sequenced on an Illumina HiSeq system with High Output chemistry v4 (50 cycles, single-read)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Data processing HiSeq Control Software 2.2.58, Basecall: RTA 1.18.64.0
FastQ generation: bcl2fastq 1.8.4, FastQ trimming: Trimmomatic 0.36 (ILLUMINACLIP:TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:3:20 MINLEN:36), alignment: tophat 2.1.0 with bowtie2 2.2.5 and samtools 0.1.19 (--no-novel-juncs)
Reads were summarized per gene using the featureCount algorithm implemented in the R package Rsubread (v1.16.1).
Raw counts of protein-coding genes were normalized either using varianceStabilizingTransformation or normTransform function of the DESeq2 package (v1.6.3) (pseudocount=1, log2-transformation).
Genome_build: iGenome Homo_sapiens/Ensembl/GRCh38
Supplementary_files_format_and_content: Raw counts - tab-deliminated file with reads summerized per gene.
Supplementary_files_format_and_content: Variancestablized transformed data (vst) - tab-deliminated file with normalized and variance stabilizing transformed data of protein-coding genes
Supplementary_files_format_and_content: Normalized data (norm) - tab-deliminated file with normalized and log2-transformed data (pseudocount=1) of protein-coding genes
 
Submission date Oct 18, 2019
Last update date Nov 01, 2019
Contact name Karsten Jürchott
E-mail(s) karsten.juerchott@charite.de
Organization name Charité - Universitätsmedizin Berlin
Department Berlin-Brandenburg Center for Regenerative Therapies
Street address Augustenburger Platz 1
City Berlin
ZIP/Postal code D-13353
Country Germany
 
Platform ID GPL20301
Series (1)
GSE139073 Multi-Parameter Analysis of Biobanked Human Bone Marrow Stromal Cells Shows Little Influence for Donor Age and Mild Comorbidities on Phenotypic and Functional Properties
Relations
BioSample SAMN13054568
SRA SRX7018643

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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