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Sample GSM538629 Query DataSets for GSM538629
Status Public on Jul 14, 2010
Title Control RNAi1-1
Sample type RNA
Source name HeLa cells, control RNAi
Organism Homo sapiens
Characteristics cell line: HeLa
cell type: human cervical cancer cells
rnai: control
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.

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.
Submission date Apr 27, 2010
Last update date Jul 14, 2010
Contact name Hank heng qi
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

Data table header descriptions
VALUE Normalized log2 value

Data table
PH_hs_0000002 8.02
PH_hs_0000003 6.63
PH_hs_0000004 9.91
PH_hs_0000005 6.53
PH_hs_0000006 7.98
PH_hs_0000007 12.52
PH_hs_0000008 9.46
PH_hs_0000009 9.87
PH_hs_0000010 14.48
PH_hs_0000011 8.58
PH_hs_0000012 8.02
PH_hs_0000013 10.03
PH_hs_0000014 7.79
PH_hs_0000015 7.4
PH_hs_0000016 7.89
PH_hs_0000017 6.76
PH_hs_0000018 8.64
PH_hs_0000019 6.67
PH_hs_0000020 15.16
PH_hs_0000021 8.07

Total number of rows: 30968

Table truncated, full table size 575 Kbytes.

Supplementary file Size Download File type/resource
GSM538629.gpr.gz 2.7 Mb (ftp)(http) GPR
Processed data included within Sample table

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