|
| Status |
Public on Apr 13, 2011 |
| Title |
shScr_3 |
| Sample type |
RNA |
| |
|
| Source name |
embryonic stem cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: embryonic stem cells
shRNA: Scrambled
|
| Treatment protocol |
Cells were lentiviral transduced with scrambled or Tet1 shRNA
|
| Growth protocol |
Low passage (p17) E14TG2a.4 feeder independent ES cells were cultured on 0.1% gelatin-coated plates in Glasgow medium (Sigma) supplemented with glutamine (Gibco), nonessential amino acids (Gibco), sodium pyruvate (Gibco), 50 ìM ßmercaptoethanol, and 15% foetal bovine serum (HyClone) in the presence of LIF. Recombinant lentiviruses encoding TET1 shRNA were produced by standard methods employing co-transfection of PLKO.1 shRNA and packaging vectors in 293FT cells. shRNA transduced ES cells were selected 36 hours post transduction with 2 ìg per ml of puromycin for 72 hours.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNAeasy (Qiagen)
|
| Label |
biotin
|
| Label protocol |
samples were processed with the Whole Transcript Assay Kit as recommended by the manufacterer (Affymetrix)
|
| |
|
| Hybridization protocol |
Affymetrix standard procedure
|
| Scan protocol |
Affymetrix standard procedure
|
| Data processing |
R/Bioconductor. 'affy' package. RMA function. Statistics performed using the 'limma' package. ANNOTATION: chip library files downloaded from Custom CDF library at bioconductor. vers13 july 6 2010. http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/CDF_download.asp. Package name mogene10stv1mmentrezg
|
| |
|
| Submission date |
Oct 20, 2010 |
| Last update date |
Apr 13, 2011 |
| Contact name |
Kristine Williams |
| E-mail(s) |
kristine.williams@bric.dk
|
| Organization name |
University of Copenhagen
|
| Department |
BRIC
|
| Lab |
Helin
|
| Street address |
Ole Maaløes vej 5
|
| City |
Copenhagen |
| ZIP/Postal code |
2200 |
| Country |
Denmark |
| |
|
| Platform ID |
GPL11078 |
| Series (2) |
| GSE24842 |
Tet1 and hydroxymethylcytosine in transcription and DNA methylation fidelity (Affymetrix gene expression data) |
| GSE24843 |
Tet1 and hydroxymethylcytosine in transcription and DNA methylation fidelity |
|
