|
| Status |
Public on Jan 04, 2012 |
| Title |
Tet1-KD ES cells siRNA #2 96hr, rep1 |
| Sample type |
RNA |
| |
|
| Source name |
E14Tg2a Embryonic Stem Cells
|
| Organism |
Mus musculus |
| Characteristics |
cell line: E14Tg2a
transfection: Tet1 siRNA #2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using RNAeasy kit (Qiagen)
|
| Label |
biotin
|
| Label protocol |
Labeling was performed using Affymetrix's IVT labeling kit following manufacturer's directions.
|
| |
|
| Hybridization protocol |
One hundred ng of total RNA was amplified as directed in the Affymetrix 3' IVT Express kit protocol, performing the IVT reaction for 16 hours. 12.5 μg of amplified biotin-aRNAs were fragmented and 10 μg were hybridized to Affymetrix 430 2.0 array for 16 hours at 45°C in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol. Array slides were stained with streptavidin/phycoerythrin utilizing a double-antibody staining procedure and then washed for antibody amplification according to the GeneChip Hybridization, Wash and Stain Kit and user manual.
|
| Scan protocol |
Arrays were scanned in an Affymetrix Scanner 3000 and data was obtained using the GeneChip® Command Console Software (AGCC; Version 1.1).
|
| Data processing |
Data was processed by performing background correction, quantile normalization, and calculation of expression set summaries using the Robust Multichip Average (RMA) protocol (Irizarry et al. (2003); Biostatistics 4: pages 249-264) as implemented in the affy packge from Bioconductor (http://www.bioconductor.org). Gene-specific probesets were constructed using the Entrez Gene – centric custom CDF, version 13 (Dai et al. (2005); Nucl Acids Res 33: e175). Log-scale data was further normalized by 1) setting the per-sample median to 6.5 and 2) subtracting the per-gene median.
|
| |
|
| Submission date |
Dec 08, 2011 |
| Last update date |
Jan 04, 2012 |
| Contact name |
Raja Jothi |
| E-mail(s) |
jothi@mail.nih.gov
|
| Organization name |
National Institutes of Health
|
| Department |
National Institute of Environmental Health Sciences
|
| Lab |
Systems Biology
|
| Street address |
111 TW Alexander Drive; A314
|
| City |
RTP |
| State/province |
NC |
| ZIP/Postal code |
27709 |
| Country |
USA |
| |
|
| Platform ID |
GPL14661 |
| Series (2) |
| GSE34267 |
Acute depletion of Tet1-dependent 5-hydroxymethylcytosine levels impairs LIF/Stat3 signaling and results in loss of embryonic stem cell identity |
| GSE34886 |
Acute depletion of Tet1-dependent 5-hydroxymethylcytosine levels impairs LIF/Stat3 signaling and results in loss of embryonic stem cell identity [expression profiling] |
|
