|
| Status |
Public on Jan 01, 2010 |
| Title |
NRO_ 6h-2 |
| Sample type |
other |
| |
|
| Source name |
P493-6 B cells
|
| Organism |
Homo sapiens |
| Characteristics |
time point: six hours
replicate: 2
sample: nuclear run-on RNA
|
| Treatment protocol |
P493-6 cells were grown in the presence or absence of tetracycline for the time periods indicated, ectopic Myc gene expression is repressed in the presence of tetracycline and induced following its removal.
|
| Growth protocol |
P493-6 cells were grown in RPMI Medium 1640 supplemented with 10% heat-inactivated fetal bovine serum, MEM non-essential amino acids, and antibiotic-antimycotic, in a humidified incubator (95% air and 5% CO2) at 37⁰C.
|
| Extracted molecule |
other |
| Extraction protocol |
Nuclear run-on RNA (following in vitro labeling) was purified using a modified Qiagen RNeasy RNA Isolation procedure. Total RNA was extracted with Trizol reagent, followed by clean-up with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.
|
| Label |
biotin
|
| Label protocol |
Nuclear run-on RNA was labeled by first adding biotin-modified UTP to isolated nuclei for 30 mins. Biotinylated nuclear run-on RNA was captured on avidin magnetic beads followed by first strand synthesis (directly on beads) and second strand synthesis (in solution). Biotinylated cRNA was supsequently prepared using the Ambion TotalPrep RNA Amplification Kit. Total RNA was labled with the Ambion TotalPrep RNA Amplification Kit according to manufacturers suggested protocols.
|
| |
|
| Hybridization protocol |
Standard Illumina hybridization protocol
|
| Scan protocol |
Standard Illumina scanning protocol
|
| Description |
NRO_ 6h-2
|
| Data processing |
The data were normalised using z transformation
|
| |
|
| Submission date |
Jul 15, 2009 |
| Last update date |
Jul 15, 2009 |
| Contact name |
chris cheadle |
| E-mail(s) |
ccheadl1@jhmi.edu
|
| Phone |
4105505984
|
| Organization name |
JHU
|
| Department |
SOM
|
| Lab |
JHBMC Genomics Core
|
| Street address |
5200 Eastern Ave
|
| City |
baltimore |
| State/province |
MD |
| ZIP/Postal code |
21224 |
| Country |
USA |
| |
|
| Platform ID |
GPL6255 |
| Series (1) |
| GSE17109 |
MYC Transactome Mapped by Global Array-based Nuclear Run-on (ANRO) |
|
