|
| Status |
Public on Jan 12, 2011 |
| Title |
Endoderm_passage6_mes1_rep2 |
| Sample type |
RNA |
| |
|
| Source name |
mouse embryonic stem cell-derived endoderm, P6
|
| Organism |
Mus musculus |
| Characteristics |
strain: R1
cell type: embryonic stem cell
|
| Treatment protocol |
The sorted Sox17-GFP(+) cells were split into 3 destinations: 1. RNA was collected (for an unpassaged, freshly-differentiated sample of endoderm) OR 2. Sox17-GFP(+) cells were serially passaged six times (P6) on mouse mesenchyme 1 OR 2. Sox17-GFP(+) cells were serially passaged six times (P6) on mouse mesenchyme 2
|
| Growth protocol |
Mouse embryonic stem cells containing a Sox17-GFP construct were differentiated using growth factors (Activin A and Wnt3A) for six days to definitive endoderm. Sox17-GFP(+) cells were sorted using fluorescence-activated cell sorting (FACS).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Sox17-GFP(+) cells were isolated by FACS in buffer containing PBS/5% FBS. Cells were spun for 5 minutes, 1000 rpm, and the supernatant was removed. RNA was then harvested using the Rneasy kit (Qiagen) according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Total RNA was amplified and labeled using the Illumina TotalPrep RNA amplification kit (Ambion).
|
| |
|
| Hybridization protocol |
Samples were hybridized onto Illumina Mouse Ref8 version 2 BeadChips as per the manufacturer's instructions.
|
| Scan protocol |
Arrays were scanned on an Illumina machine according to the manufacturer's instructions.
|
| Description |
culture condition: co-culture with mesenchyme 1
|
| Data processing |
Data were analyzed with BeadStudio analysis software (Illumina). Samples were normalized using Illumina's average normalization, with no background subtraction. The data were filtered for only genes for which the p value of detection was < 0.01.
|
| |
|
| Submission date |
Nov 15, 2010 |
| Last update date |
Jan 12, 2011 |
| Contact name |
Julie Beth Sneddon |
| Organization name |
Harvard University
|
| Department |
Department of Stem Cells and Regenerative Biology
|
| Lab |
Douglas Melton Lab
|
| Street address |
7 Divinity Avenue
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02138 |
| Country |
USA |
| |
|
| Platform ID |
GPL6885 |
| Series (1) |
| GSE25337 |
Gene expression data of Sox17-GFP(+) mouse definitive endoderm before and after expansion on mesenchyme. |
|
