|
| Status |
Public on Sep 29, 2014 |
| Title |
WT3DP |
| Sample type |
RNA |
| |
|
| Source name |
wild type MEF 3, 3h DP
|
| Organism |
Mus musculus |
| Characteristics |
cell type: primary mouse embryonic fibroblast (e14.5)
strain: C57Bl/6 x 129Sv (F1)
|
| Treatment protocol |
10ul of 100mM 2',2'-dipyridyl or ethanol vehicle was added to each plate and plates were returned to normoxia 5% CO2 incubator for 3hrs. Medium was then removed from the plates and Trizol reagent was added directly to plate.
|
| Growth protocol |
10 cm dishes of each p4 wild type and CBP/p300 compound homozygous conditional MEF were plated at 1x10^6 cells/dish in 20ml DMEM+10%FBS containing Cre recombinase expressing adenovirus at an MOI of 100 and grown in a 3% O2 5%CO2 incubator. Medium was changed 16hrs later for 10ml DMEM + 10%FBS and MEFs were grown for 48hrs in 3% O2 5%CO2 incubator. MEFs were transferred to a normoxia 5% CO2 incubator and grown for 24hrs.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using the standard Trizol instructions.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix 3’IVT Express protocol starting with 100 ng of total RNA (GeneChip 3’ IVT Express Kit 702646 Rev. 8, 2008-2010, Affymetrix)
|
| |
|
| Hybridization protocol |
Following fragmentation, 5 microgram of cRNA was hybridized for 16 hr at 45C on each array. GeneChips were washed and stained in the Affymetrix GeneTitan system.
|
| Scan protocol |
GeneChips were scanned using the Affymetrix GeneTitan system.
|
| Data processing |
Probe signals were quantile normalized and summarized by the RMA algorithm using the Affymetrix Expression Console Software v1.1
|
| |
|
| Submission date |
Jan 28, 2014 |
| Last update date |
Sep 30, 2014 |
| Contact name |
Suzanne J Baker |
| E-mail(s) |
suzanne.baker@stjude.org
|
| Organization name |
St Jude Children's Research Hospital
|
| Department |
Developmental Neurobiology
|
| Street address |
262 Danny Thomas Place
|
| City |
Memphis |
| State/province |
TN |
| ZIP/Postal code |
38105 |
| Country |
USA |
| |
|
| Platform ID |
GPL11180 |
| Series (2) |
| GSE54452 |
Expression data from wild type and CBP/p300 null MEFs +/- 3hr treatment with 100uM dipyridyl (DP) |
| GSE54454 |
Genome-wide and single-cell analyses reveal target gene context-dependent relationship between Crebbp recruitment and both constitutive and signal-responsive gene expression. |
|
