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Sample GSM2124272 Query DataSets for GSM2124272
Status Public on Oct 24, 2016
Title MG - H9 cells cultured on a matrigel coated dish for 3days with mTeSR1 medium, rep 2
Sample type RNA
 
Source name H9 cells cultured on a matrigel coated dish for 3days with mTeSR1 medium.
Organism Homo sapiens
Characteristics cell type: embryonic stem cell
tissue: in vitro
Treatment protocol The dissociated hPSCs were resuspended in mTeSR-1 medium mixed with different concentrations of PNIPAAm-β-PEG hydrogel (HG) (Mebiol Inc., Hiratsuka, Japan) supplemented with 10 µM Y-27632. HG concentrations of 61 and 76 mg ml-1 were utilized to obtain cellular matrices with stiffness properties identified as “Low HG” and “HG”, respectively.
Growth protocol H9 human embryonic stem cells (hESCs) were cultured in mTeSR-1 medium (Stem Cell Technology) supplemented with 10 µM Rho-associated coiled-coil containing protein kinase (ROCK) inhibitor Y-27632 (Wako Pure Chemical Industries, Osaka, Japan) on day 1, and the medium was changed daily.
Extracted molecule total RNA
Extraction protocol RNA was extracted from the cells using the RNeasy Mini Kit (Qiagen, Hilden, Germany) following the manufacturer recommended protocol. After culturing hPSCs in the microfluidic device, the system was placed on ice and the cells were transferred into a 1.5-mL tube. The cells were then allowed to settle to the bottom of the tube with gravity. After centrifuging for 5 min at 300 xg, the supernatants were aspirated to remove the culture medium and trypsin. The cell pellet was then treated with cell lysis buffer from the RNeasy Mini Kit. After homogenizing the lysates, 70% ethanol was added, and the mixture was applied to a spin column in a tube, and centrifuged at 8,000 xg for 15 sec. The spin column was rinsed with a washing buffer. Finally, RNase-free water was used to elute total RNA from the spin column. The total concentration of retrieved RNA was quantified using the NanoDrop 1000 spectrophotometer (Thermo Fisher Scientific), and its quality was evaluated with the BioAnalyzer 2100 and RNA 6000 Nano kit (Agilent Technologies, Santa Clara, CA, USA).
Label Cy3
Label protocol A total of 100 ng of ribonucleic acid (RNA) from each sample was amplified and labeled with cyanine 3 (Cy3) fluorescent dye to synthesize complementary viral RNA (cRNA) using a One-Color, Low Input Quick Amp Labeling Kit (Agilent Technologies, Santa Clara, CA, USA).
 
Hybridization protocol 0.6 µg of synthesized cRNA samples were hybridized to SurePrint G3 Human GE 8×60K Ver.2.0 microarrays (Agilent Technologies, Santa Clara, CA, USA).
Scan protocol Agilent DNA microarray scanner (G2565CA) was used to obtain DNA microarray images.
Description H9 cells cultured on a matrigel coated dish for 3days with mTeSR1 medium, rep 2
Data processing Data were pre-processed using limma R/Bioconductor package including RMA background correction, quantile normalisation and log2 transformation. Control probes were removed after normalisation. Detection threshold (log2) for Stemformatics graphing uses 95th percentile of negative control probe expression as per limma recommendation. Median expression is median (log2) of above-threshold expression of all non-control probes.
 
Submission date Apr 15, 2016
Last update date Feb 27, 2019
Contact name Othmar Korn
Organization name Australian Institute for Bioengineering and Nanotechnology
Street address University of Queensland
City St. Lucia
State/province Queensland
ZIP/Postal code 4067
Country Australia
 
Platform ID GPL17077
Series (1)
GSE80324 Expression profiling of cell growth on different layers

Data table header descriptions
ID_REF
VALUE Normalized signal intensity (log2)

Data table
ID_REF VALUE
A_23_P117082 12.88925131
A_33_P3246448 4.650330974
A_33_P3318220 4.227258665
A_33_P3236322 5.058954137
A_33_P3319925 5.212258405
A_21_P0000509 18.56622122
A_21_P0000744 8.918196554
A_24_P215804 8.19365541
A_23_P110167 10.17062455
A_33_P3211513 7.041218052
A_23_P103349 2.939641109
A_32_P61480 4.390415577
A_33_P3788124 5.96775738
A_33_P3414202 7.254333176
A_33_P3316686 8.169973711
A_33_P3300975 6.186761229
A_33_P3263061 12.13479841
A_33_P3261373 4.227258665
A_24_P278460 9.283381009
A_21_P0013109 3.816484727

Total number of rows: 50599

Table truncated, full table size 1255 Kbytes.




Supplementary file Size Download File type/resource
GSM2124272_AR1128_02.txt.gz 3.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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