|
| Status |
Public on Jan 31, 2012 |
| Title |
inner cell mass cells E3.5 mixed biol rep 2 |
| Sample type |
RNA |
| |
|
| Source name |
inner cell mass of the blastocyst
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57Bl/6 x C3H F1
cell type: ICMs dissected by immunosurgery
source age: E3.5
gender: mixed
|
| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA was extracted with Qiagen RNeasy kit with in-column DNAse digestion.
|
| Label |
biotin
|
| Label protocol |
mRNA was amplified using two-rounds of in vitro transcription, and lableled by incorporation of bio-UTP in the second round.
|
| |
|
| Hybridization protocol |
Standard Affymetrix hybridization protocols
|
| Scan protocol |
Standard Affymetrix scanning protocols
|
| Description |
ICMs dissected by immunosurgery
|
| Data processing |
intensities of the Affymetrix CEL files were background subtracted, quantile normalized, and summarized for each probe set into a logarithm base two intensity value using the robust multi-array average method (RMA) implemented in the Affymetrix package. Subsequently we applied the mean center global adjustment to remove apparent batch effects across the experiments to facilitate between-experiment comparisons.
|
| |
|
| Submission date |
Jan 30, 2012 |
| Last update date |
Jan 31, 2012 |
| Contact name |
Miguel Ramalho-Santos |
| E-mail(s) |
mrsantos@diabetes.ucsf.edu
|
| Organization name |
UCSF
|
| Department |
Eli and Edythe Broad Center of Regeneration Medicine
|
| Lab |
Santos lab
|
| Street address |
35 Medical Center Way
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94143 |
| Country |
USA |
| |
|
| Platform ID |
GPL81 |
| Series (1) |
| GSE35416 |
Transcriptional profiling of mouse inner cell mass of the blastocyst, primordial germ cells and cultured pluripotent stem cells |
|
