|
| Status |
Public on Nov 18, 2016 |
| Title |
FaDU_shCtrl_new_rep3 |
| Sample type |
RNA |
| |
|
| Source name |
FaDU HNSCC cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: FaDU
treatment: shControl
|
| Treatment protocol |
RNA collected 72 hours following lentiviral knockdown by shRNA for TP63 or control vector. Lentiviral production and mRNA analysis of cell lines were performed as described (Ramsey et al., 2013, JCI).
|
| Growth protocol |
Cells were maintained at 37°C in 5% CO2 in either RPMI or DMEM or DMEM/F12 supplemented with 10% FBS, penicillin, and streptomycin.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using QIAshredder and RNeasy Plus Mini kit (both Qiagen) following manufacturer’s instructions. qRT-PCR for cell line (1 μg total RNA as template) using iQTM SYBR® Green Supermix (BioRad) was performed following manufacturer’s instructions.
|
| Label |
biotin
|
| Label protocol |
First strand cDNA synthesis was generated using a T7-linked oligo-dT primer, followed by second strand synthesis. An in vitro transcription reaction was performed to generate cRNA containing biotinylated UTP and CTP, which was subsequently chemically fragmented at 95°C for 35 minutes.
|
| |
|
| Hybridization protocol |
Ten micrograms of the fragmented, biotinylated cRNA was hybridized in MES buffer (2-[N-Morpholino]ethansulfonic acid) containing 0.5 mg/ml acetylated bovine serum albumin (Sigma) to Affymetrix Human Gene 1.0 ST array (transcript (gene) version) at 45°C for 16 hours.
|
| Scan protocol |
Scans were performed on Affymetrix scanners.
|
| Description |
FaDU HNSCC cells treated with control shRNA (replicate 2)
|
| Data processing |
Raw expression values were normalized using Robust Multiarray Averaging (RMA) in the R (version 2.15.1) Bioconductor package.
|
| |
|
| Submission date |
Oct 17, 2016 |
| Last update date |
Nov 19, 2016 |
| Contact name |
Kenneth N Ross |
| E-mail(s) |
Kenneth.Ross@dfci.harvard.edu
|
| Organization name |
Dana-Farber Cancer Institute
|
| Department |
Pediatric Oncology
|
| Street address |
450 Brookline Ave., Rm M640
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL6244 |
| Series (2) |
| GSE88833 |
Microarray Samples for shTP63 in HNSCC Cells to Investigate How ACTL6A and p63 Activate Hippo-YAP in SCC |
| GSE88861 |
Cells to Investigate How ACTL6A and p63 Activate Hippo-YAP in SCC |
|
