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Sample GSM1333409 Query DataSets for GSM1333409
Status Public on Apr 17, 2014
Title #1_undiff_0hr
Sample type RNA
 
Source name undifferentiated human ES cells before treatment
Organism Homo sapiens
Characteristics cell line: khES3
cell type: undifferentiated human ES cells
culture duration: 0 hr (untreated control)
Treatment protocol khES3 cells are cultured in the presence or abesence of extracellular methionine for 5 or 24 hr (#1_undiff_5hr_compl, #1_undiff_5hr_deltaMet, #1_undiff_24hr_compl, #1_undiff_24hr_deltaMet). 0hr indicates khES3 cells just before these manipulations (#1_undiff_0hr).
Growth protocol Before the following assay, human embryonic stem cells (khES3) are grown in human ES media to 70-80% confluent. Endoderm cells are prepared by directed-differentiation of khES3 with activinA (#1_Endoderm).
Extracted molecule total RNA
Extraction protocol Total RNA was extraced using RNeasy Mini Kit, according to the manufacturer's instructions.
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (GeneChip 3' IVT Expression Kit User Manual, P/N 702646 Rev. 8, Affymetrix).
 
Hybridization protocol Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 plus 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Scan protocol GeneChips were scanned using the GeneChip Scanner 3000 7G.
Description 1_undiff_0hr
Data processing The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
 
Submission date Feb 24, 2014
Last update date Apr 19, 2014
Contact name nobuaki shiraki
E-mail(s) shiraki@bio.titech.ac.jp
Phone 81-45-924-5814
Organization name Tokyo Institute of Technology
Department School of Life Science and Technology
Street address 4259-B-25 Nagatsuta-cho, Midori-ku
City Yokohama
ZIP/Postal code 226-8501
Country Japan
 
Platform ID GPL570
Series (2)
GSE55283 Expression data from undifferentiated human ES cell line, khES3, grown using complete or methionine deprived media and ES cell derived endoderm
GSE55285 Expression data from undifferentiated human ES cell line, khES3, grown using complete, methionine, leucine or lysine deprived media and ES cell derived endoderm

Data table header descriptions
ID_REF
VALUE normalized
ABS_CALL indicating whether the transcript was present (P), absent (A), or marginal (M)
DETECTION P-VALUE

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 1453.64 P 5.16732e-05
AFFX-BioB-M_at 2042.85 P 4.42873e-05
AFFX-BioB-3_at 1238.51 P 4.42873e-05
AFFX-BioC-5_at 3412.77 P 5.16732e-05
AFFX-BioC-3_at 4629.47 P 4.42873e-05
AFFX-BioDn-5_at 10586.5 P 4.42873e-05
AFFX-BioDn-3_at 16960.8 P 5.16732e-05
AFFX-CreX-5_at 65990.9 P 5.16732e-05
AFFX-CreX-3_at 77303 P 4.42873e-05
AFFX-DapX-5_at 167.295 P 0.000339202
AFFX-DapX-M_at 1116.1 P 0.00110197
AFFX-DapX-3_at 2735.78 P 4.42873e-05
AFFX-LysX-5_at 101.265 P 0.0218835
AFFX-LysX-M_at 129.823 P 0.0336534
AFFX-LysX-3_at 404.299 P 5.16732e-05
AFFX-PheX-5_at 58.6223 A 0.17516
AFFX-PheX-M_at 171.672 P 0.00033957
AFFX-PheX-3_at 262.386 P 0.00022441
AFFX-ThrX-5_at 11.5705 A 0.834392
AFFX-ThrX-M_at 88.8897 A 0.108959

Total number of rows: 54675

Table truncated, full table size 1628 Kbytes.




Supplementary file Size Download File type/resource
GSM1333409__1_undiff_0hr.CEL.gz 3.4 Mb (ftp)(http) CEL
GSM1333409__1_undiff_0hr.CHP.gz 525.4 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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