NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2495515 Query DataSets for GSM2495515
Status Public on Mar 13, 2018
Title iMSC1_hPL-gel_without_TN [methylation]
Sample type genomic
 
Source name iMSCs, hPL-gel without TN
Organism Homo sapiens
Characteristics donor: 1
cell type: iPSC-derived MSCs (iMSCs)
passage: 5
differentiation condition: hPL-gel without thrombin (TN)
Treatment protocol 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 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 genomic DNA
Extraction protocol Genomic DNA was isolated using the Macherey-Nagel NucleoSpin Tissue Kit.
Label Cy5 and Cy3
Label protocol Standard Infinium HD Methylation Assay protocol.
 
Hybridization protocol Bisulfite-converted DNA was amplified, fragmented and hybridized to Illumina Infinium HumanMethylation450 BeadChip using standard Infinium HD Methylation Assay protocol.
Scan protocol Standard Infinium HD Methylation Assay protocol.
Data processing Initial analysis was performed by the GenomeStudio 2010.3 (Modul M Version 1.8.5). Data were normalized with internal controls according to Illumina's standard procedures. Methylation level at each locus was calculated with the GenomeStudio Methylation module as beta-value (ranging from 0 to 1). The number of beads per feature varies between chips and beta-values were calculated as average of at least three technical replica.
 
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 GPL13534
Series (2)
GSE95058 Soft Hydrogels Support Differentiation of Induced Pluripotent Stem Cells toward Mesenchymal Stromal Cells [methylation]
GSE95061 Soft Hydrogels Support Differentiation of Induced Pluripotent Stem Cells toward Mesenchymal Stromal Cells

Data table header descriptions
ID_REF
VALUE Average Beta

Data table
ID_REF VALUE
cg00000029 0.884195
cg00000108 0.963388
cg00000109 0.948759
cg00000165 0.125567
cg00000236 0.919443
cg00000289 0.701521
cg00000292 0.938383
cg00000321 0.549808
cg00000363 0.326339
cg00000622 0.028242
cg00000658 0.844748
cg00000714 0.176198
cg00000721 0.961106
cg00000734 0.087509
cg00000769 0.080739
cg00000807 0.913502
cg00000884 0.893369
cg00000905 0.137622
cg00000924 0.388027
cg00000948 0.931082

Total number of rows: 485512

Table truncated, full table size 9494 Kbytes.




Supplementary file Size Download File type/resource
GSM2495515_200109350061_R06C02_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM2495515_200109350061_R06C02_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap