|
| Status |
Public on Feb 01, 2013 |
| Title |
male T1KO#99 Replicate 2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
male Tet1 ESC
|
| Organism |
Mus musculus |
| Characteristics |
background strain: C57/BL/6
gender: male
genotype: Tet1 knockout
|
| Treatment protocol |
Feeders were separated by preplating on gelatin coated platesprior to mRNA extraction.
|
| Growth protocol |
Mouse embryonic stem cells were cultured on gamma irridiated feeders in LIF contianing medium.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using Qiagen RNAeasy Kit
|
| Label |
Cy3
|
| Label protocol |
Cy3 and Cy5-labeled cRNA was prepared using the Low Input Quick Amp labeling kit (Agilent) starting with 200ng of total RNA
|
| |
|
| Channel 2 |
| Source name |
male ESC,not included in differential expression analysis due to false genotype
|
| Organism |
Mus musculus |
| Characteristics |
genotype: n/a
background strain: C57/BL/6
gender: male
|
| Treatment protocol |
Feeders were separated by preplating on gelatin coated platesprior to mRNA extraction.
|
| Growth protocol |
Mouse embryonic stem cells were cultured on gamma irridiated feeders in LIF contianing medium.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using Qiagen RNAeasy Kit
|
| Label |
Cy5
|
| Label protocol |
Cy3 and Cy5-labeled cRNA was prepared using the Low Input Quick Amp labeling kit (Agilent) starting with 200ng of total RNA
|
| |
|
| |
| Hybridization protocol |
Agilent V2 Mouse 4x44k expression arrays were hybridized and washed according to manufacturer's instructions
|
| Scan protocol |
Agilent DNA microarray scanner was used following manufaturer's instructions
|
| Data processing |
Data were normalized within array by loess normalization and between arrays by quantile normalization of average intensities (“Aquantile”) using Bioconductor. Probes for the same gene were summarized by mean and technical replicas were combined by average
|
| |
|
| Submission date |
Dec 18, 2012 |
| Last update date |
Feb 01, 2013 |
| Contact name |
Inmaculada Barrasa |
| E-mail(s) |
[email protected]
|
| Organization name |
Whitehead Institute
|
| Street address |
Nine Cambridge Center
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
| |
|
| Platform ID |
GPL11202 |
| Series (1) |
| GSE42991 |
Gene expression profiles of Tet1 knockout (T1KO), Tet2 knockout (T2KO) and Tet1/Tet2 double knockout (DKO) mouse embryonic stem cells. |
|
