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Sample GSM5008113 Query DataSets for GSM5008113
Status Public on Jun 30, 2021
Title WJ-MSC-2D exosome treat-RNA,rep1
Sample type RNA
 
Source name hWJ-MSC, treated with 2D extracellular vesicles
Organism Homo sapiens
Characteristics cell type: Wharton's Jelly Derived Mesenchymal Stem Cells (WJ-MSCs)
treatment: 2D extracellular vesicles
Treatment protocol For transcriptome analysis, RNA was prepared from 2D and 3D cultured hMSCs, DPBS-treated, 2D EV- or 3D EV-treated cells as well as Fenbendazole or Brompheniramine-treated cells. Treatment was performed for 6 hrs. All of the treatment was independently carried out in triplicate.
Growth protocol For 2D culture, hWJ-MSCs were cultured in MEMα medium (Gibco, Grand Island, NY, USA) supplemented with 10% (v/v) FBS and 1% (v/v) antibiotic-antimycotic solution (2D medium) under 5% CO2 and 37°C conditions, and the medium was changed every 3 days. When the cells reached 80% confluence, cells were passaged using 0.25% (w/v) trypsin-EDTA (Gibco). For 3D culture of hWJ-MSCs, 3D medium was prepared by supplementing MEMα medium described above with 0.05% (v/v) Cellhesion VP (Nissan Chemical Industries, Ltd., Tokyo, Japan) according to the manufacturer’s instruction. Cells were seeded at a density of 1 × 106 cells/flask in 10 mL of 3D medium in a 125 mL non-adherent flask (Corning, Corning, NY, USA) and incubated on a rocker (LABOGENE, Seoul, Korea) at 9 rpm with mechanical dissociation daily up to 15 days under 5% CO2 and 37°C conditions. The medium was changed every 3 days. Nine days after 3D culture, primed hMSCs were retrieved by transferring the cell-Cellhesion VP aggregates to a tissue culture plate. The aggregates were spin-down at 1,500 rpm for 3 min and the supernatant was discarded. The aggregates were resuspended by pipetting in 5 mL of 2D medium, transferred to the 100 mm tissue culture plate (Corning), and subjected to cell retrieval from the aggregates. The retrieved cells were maintained in 2D culture condition until used.
Extracted molecule total RNA
Extraction protocol Total RNA from hWJ-MSCs was prepared using a RNeasy Mini kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions. During RNA preparation, DNase (Qiagen) was applied to prevent the genomic DNA contamination.
Label biotin
Label protocol The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit.
 
Hybridization protocol Approximately 5.5 μg of labeled cDNA was hybridized to the Affymetrix GeneChip Human Gene 2.0 ST Array (Affymetrix, Santa Clara, CA, USA) at 45 °C for 16 h.
Scan protocol After hybridization, the arrays were scanned on a GCS3000 Scanner (Affymetrix) and data analyses were carried out with the GeneChip Command Console Software (Affymetrix).
Data processing Expression data were normalized using the robust multi-array average (RMA) approach.
 
Submission date Jan 06, 2021
Last update date Jun 30, 2021
Contact name Eun Seo Kim
E-mail(s) eun2927@snu.ac.kr
Organization name Seoul National University
Department Department of International Agricultural Technology
Lab Systems Pharmacology Lab
Street address 25354 Pyeongchang-daero, Daehwa-myeon
City Pyeongchang-gun
ZIP/Postal code 1447
Country South Korea
 
Platform ID GPL16686
Series (1)
GSE152507 Cellhesion VP enhances the therapeutic potential of human Wharton’s jelly-derived mesenchymal stem cell-derived extracellular vesicles

Data table header descriptions
ID_REF
VALUE log2 transformed RMA normalized expression value

Data table
ID_REF VALUE
16650001 1.28175
16650003 2.20257
16650005 2.37065
16650007 1.80159
16650009 1.60409
16650011 1.69271
16650013 2.38898
16650015 2.2905
16650017 2.3035
16650019 1.63036
16650021 2.42024
16650023 1.65171
16650025 1.68053
16650027 1.91379
16650029 2.61625
16650031 3.22469
16650033 1.24765
16650035 1.43847
16650037 2.97131
16650041 2.24573

Total number of rows: 53617

Table truncated, full table size 885 Kbytes.




Supplementary file Size Download File type/resource
GSM5008113_201211_13_2D_EV_1_HuGene-2_0-st_.CEL.gz 7.5 Mb (ftp)(http) CEL
Processed data included within Sample table

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