|
| Status |
Public on Oct 25, 2012 |
| Title |
low-Myc - Replicate 1 |
| Sample type |
RNA |
| |
|
| Source name |
P493-6 cells expressing a low level of c-Myc
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: P493-6
cell type: B-cell lymphoma
|
| Treatment protocol |
c-Myc expression released for 0 hours.
|
| Growth protocol |
RPMI 1640 + FBS. Tetracycline repressed c-Myc transgene expression. c-Myc expression released for 0 hours.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
External spike-in RNAs (ERCC ExFold RNA Spike-In kit, Ambion, 4456739) were added based on cell number. See manuscript for details.
|
| Label |
biotin
|
| Label protocol |
Biotinylated aRNA was prepared according to the standard Affymetrix protocol from 100 ng total RNA (GeneChip 3' IVT Express Kit User Manual, 2009, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 12.5 ug of aRNA were hybridized at 45C for 16 hr at 60RPM on GeneChip Arrays (PrimeView). GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the manurfacturer's instructions, using the buffers provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit.
|
| Scan protocol |
GeneChips were scanned using the GeneChip Scanner 3000 and images were extracted with Affymetrix GeneChip Expression Console. A CDF containing the ERCC probes was provided by Affymetrix.
|
| Data processing |
A CDF provided by Affymetrix, which contained the ERCC probes (PrimeView_withERCC_binary.cdf) was used instead of the standard PrimeView cdf.
The data were analyzed with Bioconductor using the MAS5 normalization method. Then, these data were renormalized to the external spike-ins. See manuscript for additional details.
|
| |
|
| Submission date |
Sep 11, 2012 |
| Last update date |
May 19, 2015 |
| Contact name |
Richard A Young |
| E-mail(s) |
young_computation@wi.mit.edu
|
| Phone |
617-258-5219
|
| Organization name |
Whitehead Institute for Biomedical Research
|
| Lab |
Young Lab
|
| Street address |
9 Cambridge Center
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
| |
|
| Platform ID |
GPL16043 |
| Series (2) |
| GSE40782 |
Revisiting Global Gene Expression Analysis (Microarray) |
| GSE40784 |
Revisiting Global Gene Expression Analysis |
|
