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Sample GSM239826 Query DataSets for GSM239826
Status Public on Oct 25, 2008
Title Human embryonic stem cell line T3ES, biological rep3
Sample type RNA
 
Source name Human embryonic stem cell line hES-T3 (T3ES) with normal female karyotype (46, XX) was derived from preimplantation embryos
Organism Homo sapiens
Characteristics gender: female
passage: 36
cell line: T3ES
Treatment protocol Non
Growth protocol hES-T3 was continuously cultured on mitotically inactivated mouse embryonic fibroblast (MEF) feeder layer in hES medium under 5% CO2 at 37oC and underwent freezing/thawing processes. The hES culture medium consisted of DMEM/F12 (1:1, GIBCO) supplemented with 20% KSR, 1% non-essential amino acids, 1 mM L-glutamine, 0.1 mM £]-mercaptoethanol, and 4 ng/ml basic fibroblast growth factor (bFGF; Life Technologies). Routine passages of hES-T3 line every 5-7 days were done with collagenase ( type IV, 1 mg/ml, Invitrogen) treatment and mechanical scrape. The undifferentiated state of hES-T3 cells (passage 36) grown on MEF feeder layer was indicated by expression of OCT4 and NANOG
Extracted molecule total RNA
Extraction protocol Trizol extraction of total RNA was performed according to the manufacturer's instructions. Total RNAs extracted using TRIZOL reagent were quantified spectrophotometrically. The cDNA synthesis was carried out by using SUPERSCRIPTTM one-step RT-PCR kit (Invitrogen). For the reverse transcription step, the whole 5 ul of the resuspended RNAs were incubated for 60 min at 42oC, then 15 min at 72oC in 50 ul of reaction mixture containing 25 ul of 2x Reaction Mix (Invitrogen) and 1 ul of RT/PLANTINUM Taq Mix (Invitrogen). 28.5 ul of the cDNAs present in the 50 ul RT reaction mixture purified by Microarray Target Purification Kit (Roche Applied Science, Indianapolis, ID, USA, http://www.roche-applies-science.com) were used as templates to amplify cDNA by Microarray Target Amplification Kit. The amplified cDNAs were purified by Microarray Target Purification Kit, and complementary RNAs (cRNAs) were synthesized from 200 ng cDNA with Microarray RNA Target Synthesis Kit (Roche Applied Science).
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 micrograms purified cRNA (Expression Analysis Technical Manual, 2004, Affymetrix).
 
Hybridization protocol Following fragmentation, 10 micrograms of cRNA were hybridized for 16 hr at 45oC on Affymetrix Human Genome U133 plus 2.0 GeneChip. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Scan protocol GeneChips from the hybridization experiments were read by the Affymetrix GeneChip scanner 3000.
Description The mRNA profiles from the undifferentiated human embryonic stem cell line hES-T3 (T3ES), hES-T3 derived embryoid bodies (T3EB) and hES-T3 differentiated fibroblast-like cells (T3DF) were quantitatively determined.
Data processing The data were processed by GeneSpring software version 7.2 GC-RMA preprocessor to use on the CEL files
 
Submission date Oct 26, 2007
Last update date Aug 28, 2018
Contact name Sung-Liang Yu
E-mail(s) slyu@ntu.edu.tw
Phone 886-2-23958341
Organization name National Taiwan University
Department Clinical Laboratory Sciences and Medical Biotechnology
Lab Microarray Core Facility
Street address Jen Ai Road Section1
City Taipei
ZIP/Postal code 100
Country Taiwan
 
Platform ID GPL570
Series (2)
GSE9440 Expression data from human embryonic stem cell differentiation
GSE14503 microRNA and mRNA expression profiles of human pancreatic islet-like cell clusters
Relations
Reanalyzed by GSM871516
Reanalyzed by GSE119087

Data table header descriptions
ID_REF Affymetrix Synthetic ID
VALUE GC-RMA-calculated Signal intensity

Data table
ID_REF VALUE
1007_s_at 1.231
1053_at 1.351
117_at 0.928
121_at 0.733
1255_g_at 36.8
1294_at 0.655
1316_at 0.893
1320_at 0.981
1405_i_at 0.615
1431_at 0.656
1438_at 0.833
1487_at 1.014
1494_f_at 1
1552256_a_at 1.491
1552257_a_at 1.582
1552258_at 0.961
1552261_at 1.101
1552263_at 1.38
1552264_a_at 1.1
1552266_at 0.988

Total number of rows: 54675

Table truncated, full table size 882 Kbytes.




Supplementary file Size Download File type/resource
GSM239826.CEL.gz 5.0 Mb (ftp)(http) CEL
Processed data included within Sample table

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