NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM613188 Query DataSets for GSM613188
Status Public on Apr 04, 2011
Title HSF_rho+_4 h_control_rep1
Sample type RNA
 
Source name Skin fibroblast, normal mitochondria, control, 4 hr
Organism Homo sapiens
Characteristics cell line origin: DWFb1
cell type: human skin fibroblast immortalized with SV40 TAg
mitochondrial status: normal
treatment: none
treatment time: 4 hours
Treatment protocol Cells were exposed to 0 (sham irradiated) or 50 cGy 4He ions (125 keV per micron) using the track segment mode of the 5.5-MV Singletron accelerator.
Growth protocol Human skin fibroblasts (HSF) immortalized by SV40 T antigen were maintained in a 4.5 g/L glucose DMEM with 4 mM L-glutamine and 100 mg/L sodium pyruvate supplemented with 10% fetal bovine serum, 100 IU/ml penicillin, and 100 microg/ml streptomycin. Mitochondrial (mt) DNA-depleted rho0 cells were established from the corresponding parent rho+cells using prolonged exposure to ethidium bromide (50 ng/ml) in growth medium supplemented with 50 microg/ml uridine.
Extracted molecule total RNA
Extraction protocol RNA was isolated using Ribopure (Ambion, Applied Biosytems) according to the manufacturer’s instructions.
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 300 ng RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer’s instructions.
 
Hybridization protocol 1.5 ug of cRNA (>9 pmol Cy3 per ug cRNA) was fragmented and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) using the Gene Expression Hybridization Kit as recommended by Agilent.
Scan protocol Slides were scanned immediately using the Agilent DNA Microarray Scanner (G2505B) and default parameters of Feature Extraction Software 9.1 (Agilent).
Description HSFrhoplus_4HR_CX1
Data processing Background-corrected intensities were log2 transformed and median-normalized in BRB-ArrayTools, Version 3.7.0. Non-uniform outliers or features not significantly above background intensity in 20% or more of the hybridizations were filtered out.
 
Submission date Oct 26, 2010
Last update date Apr 04, 2011
Contact name Shanaz Adi Ghandhi
E-mail(s) shanazg@gmail.com
Phone 212-3053911
Organization name Columbia University Medical Center
Department Center for Radiological Research
Lab VC11-237
Street address 630, W 168th street
City New York
State/province NY
ZIP/Postal code 10032
Country USA
 
Platform ID GPL6480
Series (1)
GSE24945 Human skin fibroblast mitochondrial depletion, 0.5 Gy alpha-particle

Data table header descriptions
ID_REF
VALUE Log2-transformed signal intensities after normalization and filtering for missing values

Data table
ID_REF VALUE
GE_BrightCorner 16.34085464
DarkCorner 0.865803421
A_23_P215419 3.654973269
A_24_P66027 4.906929016
A_23_P145874 8.835991859
A_32_P77178 5.290472984
AT_ssH_TR_5 7.210627556
A_23_P212522 9.694561958
A_23_P127662 4.645414352
A_24_P934473 4.818350792
A_23_P253029 12.16139793
A_32_P125233 5.025500774
A_32_P29551 4.026417732
A_24_P298846 9.774288177
A_24_P801451 8.353481293
A_23_P141315 10.62110424
A_32_P89523 3.356338263
AT_ssH_PC_3 10.45035744
A_24_P704878 3.96628356
A_23_P155677 10.13566875

Total number of rows: 40742

Table truncated, full table size 977 Kbytes.




Supplementary file Size Download File type/resource
GSM613188.txt.gz 7.7 Mb (ftp)(http) TXT
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap