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Sample GSM7060225 Query DataSets for GSM7060225
Status Public on Feb 23, 2024
Title 2 - CH Pat.18
Sample type RNA
 
Source name Bone-marrow stromal cells derived cartilage discs
Organism Homo sapiens
Characteristics cell type: Bone-marrow stromal cells
Treatment protocol Chondrogenic Differentiation Chondrocyte phenotype was determined under re-differentiation. For chondrogenic re-differentiation, a pellet culture assay with chondrogenic differentiation media (ChM) was performed for 21 days in a 96 deep-well format. Briefly, 3 × 105 cells per pellet were used, and cultured in ChM composed of high glucose DMEM including L-glutamine (Sigma Aldrich, D6546, USA), dexamethasone (0.1 µM, Sigma Aldrich, D2915, USA), L-ascorbic acid (50 µg/mL, Sigma Aldrich, A8960, USA), L-proline (40 µg/mL, Sigma Aldrich, P5607, St. Louis, MO, USA) sodium pyruvate (0.1 mg/mL, AppliChem, A4859, Darmstadt, Germany) ITS (6.25 µg/mL, Sigma Aldrich, I1884, St. Louis, MO, USA), BSA (1.25 mg/mL, Sigma Aldrich, A9418, St. Louis, MO, USA), linoleic acid (5.35 µg/mL, Sigma Aldrich, L1012, St. Louis, MO, USA), penicillin (10 U/mL)/streptomycin (10 µg/mL) (Biochrom, A2213, Berlin, Germany) and recombinant human TGF-ß1 (10 ng/mL, Peprotech, 100-21-5, Cranbury, NJ, USA). Negative controls were cultured in the same medium but without TGF-ß1. Media change was performed every 3–4 days. Chondrogenic phenotype was determined by proteoglycan assay, type II collagen immunostaining, Alcian blue staining, as well as by expression of type II collagen, type X collagen, MMP13, Sox9 and aggrecan mRNAs.
Growth protocol Primary human bone marrow-derived BMSCs were isolated and cultivated. The cell culture medium was Dulbecco’s modified Eagle’s medium (DMEM) low glucose (Sigma Aldrich, D5546, USA) with 10% fetal calf serum ‘superior’ (Biochrom, S0615, Germany), 2 mM GlutaMAX™ (Gibco, Thermo Fisher Scientific, Waltham, MA, USA), penicillin (10 U/mL)/streptomycin (10 µg/mL) (Biochrom, Germany). Sub-cultured cells were seeded at 2400 cells/cm2 in cell culture flasks. Cells were counted by using CasyTT for standard cell culture and cryopreserved until further use.
Extracted molecule total RNA
Extraction protocol Ribonucleic acid (RNA) was isolated from snap-frozen cartilage organoid discs using RNeasy Mini kit (Qiagen) . Discs were homogenized prior RNA extraction with a Minilys homogenizer using ceramic beads (Precellys lysing kit; Bertin Technologies). RNA concentrations and quality were assessed using a Bioanalyzer (Agilent)
Label biotin
Label protocol Samples were labeled using Affymetrix WT PLUS Reagent Kit P/N 703147 Rev5, (Cat No. 902280);
 
Hybridization protocol Affymetrix Human Gene 2.0 ST Array (Cat No. 902112); Affymetrix GeneChip® HT hybridization, Wash and Stain Kit (Cat No. 900720); Affymetrix Genechip® fluidics station 450: protocol FS450_0002 for Cartridge Arrays
Scan protocol Arrays were scanned using Affymetrix Scanner: GCS3000; AGCC (Command Console Software AGCC 4.0.0)
Data processing Affymetrix Genexpression Console (4.0.0) using Affymetrix default analysis settings for generation of CEL-files.
 
Submission date Feb 23, 2023
Last update date Feb 23, 2024
Contact name Rodolphe Poupardin
E-mail(s) rodolphe.poupardin@pmu.ac.at
Organization name Paracelsus Medizinische Privatuniversität
Lab Institute for Cell Therapy
Street address Strubergasse 22
City Salzburg
ZIP/Postal code 5020
Country Austria
 
Platform ID GPL16686
Series (1)
GSE225903 Expression profiling of cartilage discs derived from Bone-marrow stromal cells.

Data table header descriptions
ID_REF
VALUE log2 RMA normalized values (and background substracted)

Data table
ID_REF VALUE
16650001 1.55035322
16650003 2.493634261
16650005 3.175037887
16650007 1.998502931
16650009 0.999347073
16650011 1.850600456
16650013 3.728533329
16650015 5.449645431
16650017 1.28641351
16650019 3.251732281
16650021 3.419127469
16650023 2.486544215
16650025 2.540350755
16650027 1.924686589
16650029 3.22207129
16650031 2.975295756
16650033 1.45170636
16650035 1.661403585
16650037 2.917505577
16650041 4.580605965

Total number of rows: 53617

Table truncated, full table size 1093 Kbytes.




Supplementary file Size Download File type/resource
GSM7060225_2_-_CH_Pat.18.CEL.gz 7.8 Mb (ftp)(http) CEL
Processed data included within Sample table

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