NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM625425 Query DataSets for GSM625425
Status Public on Jan 10, 2011
Title HFF-nostim,noinfection-2
Sample type RNA
 
Source name HFF, uninfected, unstimulated
Organism Homo sapiens
Characteristics tissue: Human foreskin fibroblast (HFF)
age: P<22
Treatment protocol Parasite strains were syringe lysed, washed at least once with PBS, and added to HFF monolayers for 18-24 hours. Some samples were also stimulated with human TNF for 6 hours.
Growth protocol Human foreskin fibroblasts (HFFs) were grown in T25 flasks (BD Biosciences) at 37C, 5% CO2 to confluency. Parasite strains were maintained in vitro by serial passage on monolayers of HFFs.
Extracted molecule total RNA
Extraction protocol Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Label biotin
Label protocol Labeled cDNA were prepared with the NuGEN Applause system from 50-100ng total RNA.
 
Hybridization protocol Following fragmentation, 4 ug of cDNA from uninfected samples or 5 ug of cDNA from infected samples were hybridized on GeneChip Human Genome U133A 2.0 Array in Affymetrix GeneChip Hybridization Oven 640, for 16 hours at 45C, 60rpm. Arrays were washed and stained in Affymetrix Fluidics Station 450 according to manufacturer's protocol.
Scan protocol GeneChips were scanned using the Affymetrix GeneChip Scanner 7G.
Data processing The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500. Data was then normalized, setting all data to have a minimum value of 50. Probes called absent or M were also set to have a value of 50.
 
Submission date Nov 18, 2010
Last update date Jan 10, 2011
Contact name Emily E Rosowski
E-mail(s) rosowski@mit.edu
Organization name MIT
Department Biology
Lab Saeij
Street address 77 Massachusetts Ave, 68-258d
City Cambridge
State/province MA
ZIP/Postal code 02139
Country USA
 
Platform ID GPL96
Series (2)
GSE25468 Expression data from Human foreskin fibroblasts (HFFs) infected with Toxoplasma gondii.
GSE25476 Expression data from host cells infected with different strains of Toxoplasma gondii

Data table header descriptions
ID_REF
VALUE Normalized MAS5.0 signal intensity

Data table
ID_REF VALUE
206211_at 50.00
220054_at 50.00
205476_at 50.00
203691_at 50.00
211506_s_at 50.00
41469_at 50.00
39402_at 89.50
207442_at 50.00
202859_x_at 137.10
1405_i_at 50.00
204655_at 50.00
213524_s_at 158.40
206421_s_at 333.80
211786_at 50.00
209270_at 50.00
214974_x_at 50.00
205114_s_at 50.00
220138_at 50.00
212657_s_at 50.00
205266_at 50.00

Total number of rows: 22283

Table truncated, full table size 381 Kbytes.




Supplementary file Size Download File type/resource
GSM625425.CEL.gz 2.2 Mb (ftp)(http) CEL
Processed data included within Sample table

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