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Sample GSM264885 Query DataSets for GSM264885
Status Public on May 10, 2009
Title H1hESC 3h 20%O2
Sample type RNA
 
Source name human embryonic stem cells, BMP4 3h, 20% O2
Organism Homo sapiens
Characteristics human embronic stem cell, NIH code:WA01
Treatment protocol hESC were cultured in either a standard humidified tissue culture CO2 incubator, set at 5% CO2 in air, or a sealed chamber (MIC-101, Billups-Rothenberg, Del Mar, CA) filled with the humidified physiological O2 mixture (~4 % O2/5 % CO2/92-90 % N2) in a standard tissue culture incubator at 37°C. Oxygen levels, measured by using a Bacharach CO2/O2 Analyzer (Bacharach, Model 2830), were ~19% in the standard incubator and 3.5–4.5% in the physiological O2 chamber. To minimize temporal ‘oxygen surge’ at each media change and at passage of the cells cultured under physiological O2 condition, the medium was pre-equilibrated for 24 h under physiological gas mixture. Processing cells while outside the incubator is generally completed within 30 min to minimize periodic reperfusion effects. The H1 hESC lines had been maintained in a physiological O2 atmosphere since passage 26. Total RNA was isolated after 0, 3, 12, 24, 72, and 120 h of BMP4 exposure at passage number 37 and had been maintained on Matrigel™ for 2 passages.
Growth protocol Human ESC H1 (WA01) at passage 23 was purchased from WiCell Research Institute (Madison, WI) and cultured in six-well tissue culture plates on a monolayer of γ-irradiated (8,000 cGy) mouse embryonic fibroblast (MEF) feeder cells until passage number 35. Thereafter, cells were cultured on a substratum of 1:30 dilutions of Matrigel™ in medium conditioned by MEF. The cells were used in the experiemts at passage number 37.
Extracted molecule total RNA
Extraction protocol RNA was isolated from hESCs by using RNA STAT-60 reagent (Tel-Test Inc, Friendswood, TX) according to the manufacturer's instructions. Isopropanol precipitated RNA pellets were dissolved in 35 ul of nuclease-free water and purified with spin columns of RNeasy Mini Kit (Qiagen).
Label biotin
Label protocol Biotin labeling
 
Hybridization protocol cRNA was fragmented to uniform size and verified on the Bioanalyzer. Agilent Whole Genome arrays were hybridized with the cRNA target
Scan protocol Slides were washed and scanned on an Agilent G2565 Microarray Scanner.
Description The cRNA target was hybridized to Agilent-014850 Whole Human Genome Microarrays 4x44K (G4112F). Slides were washed and scanned on an Agilent G2565 Microarray scanner, and data analyzed with Agilent Feature Extraction and GeneSpring GX v7.3.1 softwares.
Data processing Data was analyzed with Agilent Feature Extraction and GeneSpring GX v7.3.1 softwares.
 
Submission date Feb 11, 2008
Last update date Feb 09, 2009
Contact name Toshihiko Ezashi
E-mail(s) ezashit@missouri.edu
Phone 573 884-9601
Organization name University of Missouri-Columbia
Department Animal Sciences
Lab R.M. Roberts
Street address 240a CS Bond Life Sciences Center
City Columbia
State/province MO
ZIP/Postal code 65211
Country USA
 
Platform ID GPL6480
Series (1)
GSE10469 Time course progression of BMP4-treated hESC gene expressions under 4 % and 20 % oxygen conditions.

Data table header descriptions
ID_REF
VALUE Intensity values are normalized to the median intensity of the array.

Data table
ID_REF VALUE
A_32_P99942 0.05
A_32_P99933 0.02
A_32_P99902 5.69
A_32_P99864 0.44
A_32_P9986 0.06
A_32_P99825 0.04
A_32_P99804 0.32
A_32_P99753 0.68
A_32_P99744 0.06
A_32_P99715 0.27
A_32_P99700 0.10
A_32_P99690 1.23
A_32_P99648 0.43
A_32_P99638 0.08
A_32_P9963 4.15
A_32_P99549 0.23
A_32_P99533 0.34
A_32_P99492 1.46
A_32_P99461 0.96
A_32_P99444 0.04

Total number of rows: 41000

Table truncated, full table size 713 Kbytes.




Supplementary file Size Download File type/resource
GSM264885.txt.gz 6.5 Mb (ftp)(http) TXT
Processed data included within Sample table

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