|
| Status |
Public on Nov 21, 2014 |
| Title |
low-MYCN-rep1_SHSY5Y_DMSO |
| Sample type |
RNA |
| |
|
| Source name |
SHSY5Y
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Neuroblastoma
|
| Treatment protocol |
100 nM THZ1 or DMSO for 6hrs. 1 uM Actinomycin D for 6hrs.
|
| Growth protocol |
RPMI 1640 + FBS.
|
| 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.
|
| Description |
Gene expression data
|
| 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 |
Oct 27, 2014 |
| Last update date |
Nov 21, 2014 |
| Contact name |
Rani George |
| E-mail(s) |
[email protected]
|
| Phone |
617-632-5281
|
| Organization name |
Dana Farber Cancer Institute
|
| Department |
Pediatric Oncology
|
| Lab |
Rani George Lab
|
| Street address |
450 Brookline Ave
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL16043 |
| Series (2) |
| GSE62724 |
Targeting of Super-Enhancer-Associated Oncogenic Transcription in MYCN-driven tumor cells by CDK7 inhibition [Gene Expression] |
| GSE62726 |
Targeting of Super-Enhancer-Associated Oncogenic Transcription in MYCN-driven tumor cells by CDK7 inhibition |
|
