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Sample GSM1435064 Query DataSets for GSM1435064
Status Public on Dec 31, 2014
Title VSMC SA001 day13 batch co_c
Sample type RNA
 
Source name Human Embryonic Stem Cell line SA001 from Cellartis AB differentiated into Vascular Smooth Muscle Cells; batch co_c
Organism Homo sapiens
Characteristics phenotype: normal-VSMC_day13
Treatment protocol cells were flash frozen and stored at -80°C until RNA extraction
Growth protocol Primary endothelial and vascular smooth muscle cells were cultured at 37°C, 5% CO2 and 95% humidity in EGM2 medium (Lonza) until they reached a confluency of maximal 80%.
The Human Embryonic Stem Cell line SA001 (Cellartis AB) was cultured in Priming Medium, consisting N2B27 medium (1:1 mixture of DMEM:F12 (1:1) with Glutamax (Invitrogen) and Neurobasal media supplemented with N2 and B27 (all Invitrogen)) with 1 μM CP21R7 (Roche) and 25 ng/ml BMP4 (R&D Systems)
For differentiation into VSMCs, Human Embryonic Stem Cell line SA001 was cultured in VSMC Induction Medium consisting of N2B27 medium supplemented with 10ng/ml PDGF-BB and 2ng/ml Activin
For differentiation into VSMCs, Human Embryonic Stem Cell line SA001 was cultured in VSMC Expansion Medium consisting of N2B27 with 2ug/ml Heparin and 2ng/ml ActivinA
For differentiation into ECs, Human Embryonic Stem Cell line SA001 was cultured in EC Induction Medium consisting of StemPro-34 SFM medium (Invitrogen) supplemented with 200ng/ml VEGF (PeproTech) and 2μM Forskolin (Sigma-Aldrich)
For differentiation into ECs, Human Embryonic Stem Cell line SA001 was cultured in EC Expansion Medium consisting of StemPro-34 SFM supplemented with 50 ng/ml VEGF
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) . DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer (Agilent Technologies Inc., Santa Clara, CA, USA).
Label Cy3
Label protocol Labeling was performed using 5 ug of total RNA input following the standard operating protocol of NimbleGen Systems Inc., Madison, WI USA. See www.nimblegen.com.
 
Hybridization protocol Hybridization was performed following the standard operating protocol of NimbleGen Systems Inc., Madison, WI USA. See www.nimblegen.com.
Scan protocol Scanning was performed on a NimbleGen MS200 Microarray Scanner at 2 μm pixel resolution following the standard operating protocol of NimbleGen Systems Inc., Madison, WI USA. See www.nimblegen.com.
Description VSMCs in vitro differentiated from HESC SA001 depleted with CD144 Microbeads and an autoMACSpro (Miltenyi Biotec) and cultivated in VSMC Expansion Medium on collagen coated wells (Biocoat, BD Bioscience). Total cultivation time starting from HESC plating is 13 days (day 13). It is the thrid of three wild-type replicates used in this experiment, each from separate cultures.
Data processing The raw data (.pair file) was subjected to background correction, quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249) as implemented in the NimbleScan software package, version 2.6 (Roche NimbleGen, Inc.).
 
Submission date Jul 11, 2014
Last update date Dec 31, 2014
Contact name Tobias Heckel
E-mail(s) tobias-heckel@t-online.de
Organization name Roche
Department pRED
Lab Safety Genetics & Genomics
Street address Grenzacherstr. 124
City Basel
ZIP/Postal code CH-4070
Country Switzerland
 
Platform ID GPL16025
Series (1)
GSE59326 Expression profiling in primary and stem-cell derived Human Endothelial and Vascular Smooth Muscle Cells

Data table header descriptions
ID_REF
VALUE RMA-normalized, averaged gene-level signal intensity

Data table
ID_REF VALUE
AB000409 2243.3983
AB000463 1573.4966
AB000781 1803.2059
AB001328 90.6172
AB002294 2328.1708
AB002308 9752.0876
AB002311 6086.0674
AB002313 20903.9529
AB002360 686.8098
AB002377 1502.5026
AB002381 2080.0803
AB002382 9625.6003
AB002384 169.2291
AB003177 4538.9531
AB003333 5380.1917
AB006589 80.2664
AB006590 68.8795
AB006621 539.9624
AB006625 47.1747
AB007457 2033.174

Total number of rows: 45033

Table truncated, full table size 838 Kbytes.




Supplementary file Size Download File type/resource
GSM1435064_545387_A12_532.pair.gz 2.9 Mb (ftp)(http) PAIR
GSM1435064_545387_A12_532_RMA.calls.gz 3.2 Mb (ftp)(http) CALLS
Processed data included within Sample table
Processed data provided as supplementary file

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