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Sample GSM2495551 Query DataSets for GSM2495551
Status Public on Mar 13, 2018
Title MSC1_in hPL-gel_with_TN [expression]
Sample type RNA
 
Source name MSCs, within hPL-gel with TN
Organism Homo sapiens
Characteristics donor: 1
cell type: mesenchymal stell cells (MSCs)
passage: 5
culture condition: within hPL-gel with thrombin (TN)
Treatment protocol To determine the impact of culture conditions on gene expression of primary MSCs, we treated the cells for three weeks in parallel with the following conditions: i) MSC were cultured on tissue culture plastic (TCP) in standard medium supplemented with 10% human platelet lysate (hPL-medium); ii) on TCP in hPL-plasma (after depletion of coagulation factors); iii) on hPL-gel generated without thrombin (TN), iv) on hPL-gel generated with TN (Sigma Aldrich, Hamburg, Germany), or iv) by trapping of the cells within hPL-gel with addition of TN. Alternatively, iPSCs were differentiated toward MSCs with the following conditions: iPSCs were either seeded on TCP with i) MSC standard medium supplemented with 10% human platelet lysate (hPL-medium) or ii) hPL-plasma (after depletion of coagulation factors); or on hPL-gel generated iii) without thrombin (TN) or iv) with TN (Sigma Aldrich, Hamburg, Germany) for a period of 35 days.
Growth protocol MSCs were isolated from bone marrow after written consent using guidelines approved by the Ethic Committee on the Use of Human Subjects at the University of Aachen (permit number: EK128/09). For some of the profiles, the MSCs were reprogrammed into iPSCs. To this end, MSCs of three different donors (passage 2) were infected with pCXLE-based episomal plasmids (Addgene, Cambridge, MA, USA) carrying the OCT3/4, SOX2, KLF4, LIN28 and c-MYC genes. Established iPSCs were cultured on TCP coated with vitronectin (0.5 µg/cm²) in StemMACS iPS-Brew XF (all Miltenyi Biotec GmbH, Bergisch Gladbach, Germany).
Extracted molecule total RNA
Extraction protocol RNA was isolated using the Macherey-Nagel RNA Plus kit.
Label biotin
Label protocol Standard Illumina protocol.
 
Hybridization protocol Standard Illumina protocol.
Scan protocol Standard Illumina protocol.
Data processing Raw data were quantile normalized using the GenomeStudio Software (Illumina, San Diego, USA). For comparison of gene expression of iMSCs and MSCs, all transcripts with a detection p > 0.01 were excluded.
 
Submission date Feb 18, 2017
Last update date Mar 13, 2018
Contact name Wolfgang Wagner
E-mail(s) wwagner@ukaachen.de
Phone +49 241 8088611
Organization name RWTH Aachen University
Department Helmholtz Institute for Biomedical Engineering
Lab Stem Cell Biology and Cellular Engineering
Street address Pauwelsstrasse 20
City Aachen
ZIP/Postal code 52074
Country Germany
 
Platform ID GPL10558
Series (2)
GSE95060 Soft Hydrogels Support Differentiation of Induced Pluripotent Stem Cells toward Mesenchymal Stromal Cells [expression]
GSE95061 Soft Hydrogels Support Differentiation of Induced Pluripotent Stem Cells toward Mesenchymal Stromal Cells

Data table header descriptions
ID_REF
VALUE Normalized signal intensity
Detection Pval

Data table
ID_REF VALUE Detection Pval
ILMN_1762337 102.0002 0.9376624
ILMN_2055271 123.2762 0.08961039
ILMN_1736007 108.8233 0.6805195
ILMN_2383229 113.7143 0.4402598
ILMN_1806310 126.3612 0.04415584
ILMN_1779670 110.9243 0.5636364
ILMN_1653355 122.2787 0.1077922
ILMN_1717783 107.7328 0.7272727
ILMN_1705025 107.5276 0.7415584
ILMN_1814316 116.1466 0.3103896
ILMN_2359168 96.40885 0.9909091
ILMN_1731507 111.6071 0.5376623
ILMN_1787689 109.4437 0.6454545
ILMN_3241953 171.9736 0.00
ILMN_1745607 144.9016 0.00
ILMN_2136495 101.4911 0.9441559
ILMN_1668111 100.7195 0.9597403
ILMN_2295559 123.5527 0.08831169
ILMN_1735045 516.543 0.00
ILMN_1680754 133.5423 0.01038961

Total number of rows: 47313

Table truncated, full table size 1404 Kbytes.




Supplementary file Size Download File type/resource
GSM2495551_200073360059_I_Grn.idat.gz 1.6 Mb (ftp)(http) IDAT
Processed data included within Sample table

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