|
| Status |
Public on Mar 28, 2008 |
| Title |
Day-3EB-Exp1 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
embryonic stem cell, embryoid body, day 3
|
| Organism |
Mus musculus |
| Characteristics |
embryoid body formation
|
| Treatment protocol |
medium used was ES-Diff (Same as ES-MEM but without sodium pyruvate and without LIF). Three conditions were used for cell differentiation: Embryoid Body (EB) formation, where the cells were cultured in non-adherent plastic dishes, Gelatin coated plates (GEL) where cells were cultured on plates coated with a solution at 0.1% gelatin and Matrigel coated plates (MAT) where the plates were treated with a 0.1% protein Matrigel
|
| Growth protocol |
Standard growth protocol.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total Rna Isolation mini-kit from Agilent
|
| Label |
Cy3
|
| Label protocol |
Low RNA input Fluorescent linear amplification kit
|
| |
|
| Channel 2 |
| Source name |
REFERENCE_RNA
|
| Organism |
Mus musculus |
| Characteristics |
total RNA was pooled from R1 cells differentiating with embryoid body formation protocol. Samples of equal amounts of RNA from days 1 through 7 were mixed, and this was used as REFERENCE RNA.
|
| Treatment protocol |
medium used was ES-Diff (Same as ES-MEM but without sodium pyruvate and without LIF). Three conditions were used for cell differentiation: Embryoid Body (EB) formation, where the cells were cultured in non-adherent plastic dishes, Gelatin coated plates (GEL) where cells were cultured on plates coated with a solution at 0.1% gelatin and Matrigel coated plates (MAT) where the plates were treated with a 0.1% protein Matrigel
|
| Growth protocol |
cells were cultured on gelatin-coated flasks in ES-MEM medium (DMEM high glucose, 0.1 mM non-essential amino acids, 1 mM sodium pyruvate, 100 mM 2-ME, 2 mM L-glutamine, 15% fetal bovine serum, penicillin/streptomycin 50 mg/ml each, and 1000 U LIF/ml). All cell cultures were carried out in a humidified incubator at 37ºC with 5% CO2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total Rna Isolation mini-kit from Agilent
|
| Label |
Cy5
|
| Label protocol |
Low RNA input Fluorescent linear amplification kit
|
| |
|
| |
| Hybridization protocol |
Agilent 60-mer oligo microarray processing protocol
|
| Scan protocol |
Slides were scanned using the Agilent Microarray Scanner G2565BA
Agilent’s Feature Extraction software (G2567AA, version 7.2) was used to identify spot and feature outliers. Spot quality was assessed and, if not discarded, multiple spots of the same gene were averaged (geometric mean).
|
| Description |
R1_Embryonic_Stem_Cell_Embryoid_Body_Day_3
|
| Data processing |
SNNLERM-algorithm was used to calculate normalized signal intensity ratios and confidence levels
|
| |
|
| Submission date |
Jul 24, 2007 |
| Last update date |
Aug 14, 2011 |
| Contact name |
Dario Sepulveda |
| E-mail(s) |
dsepulve@ing.uchile.cl
|
| Organization name |
Universidad de Chile
|
| Department |
Chemical Engineering and Biotechnology
|
| Lab |
CIByB
|
| Street address |
Beacuhef 861
|
| City |
Santiago |
| State/province |
RM |
| ZIP/Postal code |
8370456 |
| Country |
Chile |
| |
|
| Platform ID |
GPL891 |
| Series (1) |
| GSE8574 |
Mouse embryonic stem cell line R1 differentiation study |
|
