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Sample GSM637758 Query DataSets for GSM637758
Status Public on Feb 03, 2011
Title HUES1
Sample type RNA
 
Source name Human ES cell line HUES1, harvested at passage 28
Organism Homo sapiens
Characteristics cell line: HUES1
Sex: female
passage number: 28
Treatment protocol Embryoid body (EB) differentiation was performed as follows: Undifferentiated cells were harvested using dispase or trypsin and plated in suspension in low-adherence plates in the presence of human ES cell culture media without bFGF and plasmanate. Cell aggregates (EBs) were allowed to grow for a total of 16 days, refreshing media every 48h.
Growth protocol The pluripotent cell lines were grown in human ES media consisting of KO-DMEM (Invitrogen), 10% KOSR (Invitrogen), 10% plasmanate (Talecris), 1% glutamax or L-glutamin, non-essential amino acids, penicillin/streptomycin, 0.1% 2-mercaptoethanol and 10-20ng/ml bFGF. All pluripotent cells were grown on a monolayer of irradiated CF1-MEFs (GlobalStem) and passaged using trypsin (0.05%) or dispase (Invitrogen). Before collection of RNA for analysis, ES and iPS cells were either isolated using trypsin (0.05%) or dispase, or plated on matrigel (BD Biosciences) for one passage and fed with human ES cell media conditioned in CF1-MEFs for 24h.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using RNeasy kit (Qiagen) according to manufacturer’s recommendation.
Label biotin
Label protocol Total RNA from the samples was normalized to 50 ng/ul and the GeneChip 3’ IVT Express Protocol was used for amplification in a semi automated process. The total RNA underwent reverse transcription to synthesize first-strand cDNA. This cDNA was then converted into a double-stranded DNA template for transcription. In vitro transcription synthesized aRNA and incorporated a biotin-conjugated nucleotide. The aRNA was then purified to remove unincorporated NTPs, salts, enzymes, and inorganic phosphate. Fragmentation of the biotin-labeled aRNA prepared the samples for hybridization on the microarray.
 
Hybridization protocol The hybridization and subsequent washing and staining were performed on the Affymetrix GeneChip® Array Station (GCAS) automation platform.
Scan protocol The microarrays were scanned on the GeneChip® HT Array Plate Scanner (Affymetrix 00-0332).
Description Cultured under normal growth conditions
Data processing The data were normalized using GCRMA and Bioconductor 2.4 with default parameters.
 
Submission date Dec 09, 2010
Last update date Feb 03, 2011
Contact name Christoph Bock
E-mail(s) cbock@cemm.oeaw.ac.at
Organization name CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences
Street address Lazarettgasse 14
City Vienna
ZIP/Postal code 1090
Country Austria
 
Platform ID GPL3921
Series (1)
GSE25970 Reference maps of human ES and iPS cell variation enable high-throughput characterization of pluripotent cell lines

Data table header descriptions
ID_REF
VALUE GCRMA-normalized signal intensity

Data table
ID_REF VALUE
1007_s_at 8.813346962
1053_at 7.911721541
117_at 2.197993087
121_at 3.796375514
1255_g_at 7.086108361
1294_at 2.214528474
1316_at 3.140844258
1320_at 2.197929431
1405_i_at 2.212797619
1431_at 2.197929431
1438_at 2.20211633
1487_at 4.707999704
1494_f_at 2.237158995
1598_g_at 5.398612278
160020_at 3.430979449
1729_at 2.197958659
1773_at 2.342140422
177_at 2.197929431
179_at 2.564283735
1861_at 4.155591862

Total number of rows: 22277

Table truncated, full table size 497 Kbytes.




Supplementary file Size Download File type/resource
GSM637758.cel.gz 2.7 Mb (ftp)(http) CEL
Processed data included within Sample table

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