|
| Status |
Public on Feb 11, 2006 |
| Title |
E14_RetinoicAcid_Day2_rep2 |
| 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 |
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.
|
| |
|
| 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 |
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.
|
| |
|
| |
| 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 |
|
