|
| Status |
Public on Mar 03, 2011 |
| Title |
H1 control in TeSR1 (Control_102540) |
| Sample type |
mixed |
| |
|
| Channel 1 |
| Source name |
Undifferentiated H1 cells cultured in TeSR1 medium. The starting point of this experiment.
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: H1
passage: 33
cell type: human embryonic stem cell
treatment: H1 control in TeSR1
|
| Treatment protocol |
Cells were dissociated by TrpLE (Invitrogen) and plated into TeSR1 medium +BMP4 or TeSR1 medium -FGF2 +BMP4 to initiate differentiation. Different concentrations of BMP4 were used according to expreimental descriptions. Cells were collected at various time points during time course experiments.
|
| Growth protocol |
H1 ES cells were maintained in defined TeSR1 medium on Matrigel plates.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using RNeasy kit (Qiagen) with on-column DNAse (Qiagen).
|
| Label |
Cy5
|
| Label protocol |
Amino Allyl labeling method
|
| |
|
| Channel 2 |
| Source name |
undifferentiated H1
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: undifferentiated H1
cell line: H1
|
| Treatment protocol |
Cells were dissociated by TrpLE (Invitrogen) and plated into TeSR1 medium +BMP4 or TeSR1 medium -FGF2 +BMP4 to initiate differentiation. Different concentrations of BMP4 were used according to expreimental descriptions. Cells were collected at various time points during time course experiments.
|
| Growth protocol |
H1 ES cells were maintained in defined TeSR1 medium on Matrigel plates.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Total RNA was extracted using RNeasy kit (Qiagen) with on-column DNAse (Qiagen).
|
| Label |
Cy3
|
| Label protocol |
Amino Allyl labeling method
|
| |
|
| |
| Hybridization protocol |
Array hybridization, wash were performed according to NimbleGen’s recommended protocol
|
| Scan protocol |
Arrays were scanned using a GenePix 4000B scanner and the PMT settings were followed by NimbleGen array manual
|
| Description |
the second channel (genomic DNA) serve as common reference across the experiments
|
| Data processing |
1. Image extraction: NimbleScan provided by NimbleGen is used to extract signal data from image files (*.TFF). Signal meansurements were saved in .pair files. 2. Normalization: Signal intensities from RNA and gDNA samples are normalized with Robust Multiple-chip Analysis (RMA) algorithm (Irizarry et al., 2003) separately. A median-adjusted ratio is calculated for each gene by dividing its signal intensity from the RNA sample by the sum of the corresponding signal intensity from the gDNA sample and median signal intensity of all genes from the gDNA channel.
|
| |
|
| Submission date |
Dec 09, 2010 |
| Last update date |
Mar 03, 2011 |
| Contact name |
James Thomson |
| E-mail(s) |
JThomson@Morgridgeinstitute.org
|
| Phone |
608-263-3585
|
| Fax |
608-265-8984
|
| Organization name |
Mogridge Institute for Research
|
| Department |
Regenerative Biology
|
| Street address |
425 Henry Mall
|
| City |
madison |
| State/province |
Wisconsin |
| ZIP/Postal code |
53706 |
| Country |
USA |
| |
|
| Platform ID |
GPL6602 |
| Series (1) |
| GSE25973 |
FGF2 sustains NANOG and switches the outcome of BMP4 induced human embryonic stem cell differentiation |
|
