|
| Status |
Public on Jan 29, 2018 |
| Title |
38_SHS-Y5Y_1 |
| Sample type |
RNA |
| |
|
| Source name |
SHS-Y5Y_neuroblastoma cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: SH-SY5Y
cell type: neuroblastoma cell line
|
| Growth protocol |
Neuroblastoma cell lines were cultured in DMEM supplemented with 10% FBS.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Prior to RNA isolation, cell numbers were determined and total RNA isolation was performed using the miRvana miRNA total RNA isolation kit (ThermoFisher Scientific, AM1560) according to manufacturers instructions. Following isolation, RNA was digested with DNase (Ambion). During isolation, external RNA spike-ins (ERCC, Ambion) were added at the time of cell lysis.
|
| 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 profiling in SHS-Y5Y, rep1
|
| 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 nomalization method. Then, these data were renormalized to the external spike-ins. See manuscript for additional details.
|
| |
|
| Submission date |
Apr 11, 2016 |
| Last update date |
Jan 29, 2018 |
| Contact name |
James Bradner |
| E-mail(s) |
bradner_computation@dfci.harvard.edu
|
| Organization name |
Dana-Farber Cancer Institute
|
| Department |
Medical Oncology
|
| Lab |
Bradner Lab
|
| Street address |
450 Brookline
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL16043 |
| Series (2) |
| GSE80149 |
Enhancer invasion shapes MYCN dependent transcriptional amplification in neuroblastoma [ARRAY] |
| GSE80154 |
Enhancer invasion shapes MYCN dependent transcriptional amplification in neuroblastoma |
|
