|
| Status |
Public on Jul 14, 2010 |
| Title |
PHF8 RNAi1-1 |
| Sample type |
RNA |
| |
|
| Source name |
HeLa cells, PHF8 RNAi
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HeLa
cell type: human cervical cancer cells
rnai: PHF8
|
| Treatment protocol |
HeLa cells were transfected with pBabe control or PHF8 shRNA and puromycin-selected for more than 6 days. The stable cell lines of control and PHF8 RNAi were retransfected with the corresponding shRNA for an additional three days.
|
| Growth protocol |
HeLa cells were cultured in DMEM medium with 10% FBS.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNAs were isolated by Trizol lysis, chloroform separation and isopropanol precipitation. Obtained RNAs were further cleaned with Qiagen RNeasy Mini Kit (Cat. No.: 74104). Total RNA was isolated from triplicate cell cultures.
|
| Label |
Cy5
|
| Label protocol |
RNAs were labeled with Cy5. The reactive amino group of 5-(3-aminoallyl)-UTP/5-(3-aminoallyl)-dUTP was used to conjugate the purified aRNA/cDNA with the NHS-CyDye.
|
| |
|
| Hybridization protocol |
Hybridization was carried out to a human Oligo Microarray (Phalanx Human Whole Genome OneArray, Phalanx Biotech) according to the manufacturer's protocol. Technical duplicates were performed.
|
| Scan protocol |
After hybridization, arrays were scanned using a Molecular Dynamics™ Axon 4100A scanner. Raw intensity signals for each microarray were measured using GenePix Pro™ 6.0 software (Molecular Devices) and stored in GPR format.
|
| Description |
Biological replicate 1 of 3. Technical replicate 1 of 2.
H03-0607003390
|
| Data processing |
The data from all microarrays in each experimental set were passed to Omicsoft Array Studio software, control and missing features were removed, and the remaining signals were quantile normalized and transformed to log2 values.
Testing was performed by combining technical replicates and performing a standard student's T-test to calculate P-values. Adjusted P-values were calculated using the Benjamini and Hochberg method with a false discovery rate a-value of 0.05. Fold changes were calculated based on the mean values of the technical replicates for each probe.
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| |
|
| Submission date |
Apr 27, 2010 |
| Last update date |
Jul 14, 2010 |
| Contact name |
Hank heng qi |
| E-mail(s) |
hank_qi@hms.harvard.edu
|
| Phone |
617-6450072
|
| Fax |
617-4326687
|
| Organization name |
Harvard Medical School
|
| Department |
Pathology
|
| Lab |
Yang Shi
|
| Street address |
NRB 854, 77 Ave. Louis Pasteur
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL6254 |
| Series (1) |
| GSE21555 |
The mental retardation gene PHF8 mediates histone H4K20/H3K9 demethylation and regulates zebrafish brain apoptosis and craniofacial development: expression analysis |
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