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Sample GSM96301 Query DataSets for GSM96301
Status Public on Feb 11, 2006
Title E14_RetinoicAcid_Day2_rep1
Sample type RNA
 
Channel 1
Source name E14TG2a mouse embroyonic stem cells (ATCC, CRL-1841)
Organism Mus musculus
Characteristics mouse embryonic stem cell
Extracted molecule total RNA
Extraction protocol Mouse embryonic stem cells were induced to differentiate under three conditions treated with different chemicals (0.1µM retinoic acids (RA), 1% dimethyl sulfoxide (DMSO) or 3mM hexa-methylene-bis-acetamide (HMBA)), subject to RNA extraction by Trizol and further purified by Qiagen RNeasy kit.
Label Cy3
Label protocol 20ug total RNA was subject to dT(20) Reverse Transcription along with aminoally-dUTP. The resultant cDNA was subject to RNA hydrolysis, followed by Microcon30 clean-up. The cleaned aminoally-cDNA was coupled with NHS-ester Cy dyes and further purified with Qiaquick PCR purification kit.
 
Channel 2
Source name E14 non-treated cells
Organism Mus musculus
Characteristics E14 non-treated cells
Extracted molecule total RNA
Extraction protocol Mouse embryonic stem cells were induced to differentiate under three conditions treated with different chemicals (0.1µM retinoic acids (RA), 1% dimethyl sulfoxide (DMSO) or 3mM hexa-methylene-bis-acetamide (HMBA)), subject to RNA extraction by Trizol and further purified by Qiagen RNeasy kit.
Label Cy5
Label protocol 20ug total RNA was subject to dT(20) Reverse Transcription along with aminoally-dUTP. The resultant cDNA was subject to RNA hydrolysis, followed by Microcon30 clean-up. The cleaned aminoally-cDNA was coupled with NHS-ester Cy dyes and further purified with Qiaquick PCR purification kit.
 
 
Hybridization protocol 18uL of Cy-dye coupled cDNA was mixed with 22uL DIG Easy Hyb buffer and 4uL Herring Sperm DNA. 38uL of the mixture was loaded onto the microarray and subject to 42C incubation on MAUI hyb station for 16-20hours. The microarray was subsequently washed in 2xSSC/1%SDS, 1xSSC, 0.2xSSC and 0.05xSSC at room temperature.
Scan protocol The microarray slides were scanned with Genepix 4000B scanner (Axon Instruments, Amersham Biosciences) according to the manual
Description E14 non-treated cells used as reference for all dual-channel co-hybridisation; readout ratios provided below have all been adjusted to Sample vs Reference, regardless of the dye-swap replicates
Data processing Global median normalization
 
Submission date Feb 09, 2006
Last update date Oct 28, 2012
Contact name Huck Hui Ng
E-mail(s) nghh@gis.a-star.edu.sg
Phone +65 64788145
Fax +65 64789004
URL http://www.gis.a-star.edu.sg
Organization name Genome Institute of Singapore
Department Cell and Medical Biology
Lab Cell and Medical Biology
Street address 60 Biopolis street, #02-01 Genome
City Singapore
State/province Singapore
ZIP/Postal code 138672
Country Singapore
 
Platform ID GPL3440
Series (1)
GSE4189 The Oct4 and Nanog transcription network that regulates pluripotency in mouse embryonic stem cells

Data table header descriptions
ID_REF Well_ID
VALUE log2-transformed normalised sample vs reference signal ratio

Data table
ID_REF VALUE
1098881
1115875
1099357 0.8604
1109083 0.5215
1101041 0.6854
1106270 0.4103
1103136 0.2675
1106912 0.2691
1098661 0.5292
1094637 0.2007
1114463
1114462
1099664 0.4407
1100593 0.7421
1115693 -0.3696
1095398 0.1957
1113516 -0.987
1101533 0.6261
1113515 -0.581
1095402 0.3008

Total number of rows: 21106

Table truncated, full table size 309 Kbytes.




Supplementary file Size Download File type/resource
GSM96301.gpr.gz 2.0 Mb (ftp)(http) GPR

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