GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM1080539 Query DataSets for GSM1080539
Status Public on Aug 20, 2013
Title Toxoplasma gondii RH-JSR 1
Sample type RNA
Source name HFF + RH-JSR, 24 hours
Organism Toxoplasma gondii
Characteristics tissue: Human foreskin fibroblast
treatment: infected with RH-JSR for 24 hours
Treatment protocol Parasite strains were syringe lysed, washed once with PBS, and added to HFF monolayers for 24 hours.
Growth protocol Human foreskin fibroblasts were grown in 6 well plates at 37C, 5% CO2 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, 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 was analyzed with Robust Multi-array Average (RMA), together with Toxoplasma gondii arrays from two other studies (Khan et al, 2009 and Bahl et al, 2010) using default Affymetrix settings in Expression Console version 1.1. The log2 transformed values obtained were then set to minimum of 6.5 or higher.
Submission date Feb 08, 2013
Last update date Aug 20, 2013
Contact name Ninghan Yang
Organization name MIT
Department Biology
Lab Saeij
Street address 77 Massachusetts Ave, 68-270
City Cambridge
State/province Massachusetts
ZIP/Postal code 02139
Country USA
Platform ID GPL16542
Series (2)
GSE44191 Parasite gene expression differences between RH-ERP, RH-JSR and GT1 of Toxoplasma gondii.
GSE44246 Human foreskin fibroblasts (HFFs) infected with type I strains of Toxoplasma gondii

Data table header descriptions
VALUE normalized log2 RMA signal intensity

Data table
AFFX-BioB-5_at 8.81
AFFX-BioB-M_at 9.1
AFFX-BioB-3_at 8.95
AFFX-BioC-5_at 10.12
AFFX-BioC-3_at 9.51
AFFX-BioDn-5_at 11.1
AFFX-BioDn-3_at 12.17
AFFX-CreX-5_at 13.22
AFFX-CreX-3_at 13.39
AFFX-DapX-5_at 6.5
AFFX-DapX-M_at 6.5
AFFX-DapX-3_at 6.5
AFFX-LysX-5_at 6.5
AFFX-LysX-M_at 6.5
AFFX-LysX-3_at 6.5
AFFX-PheX-5_at 6.5
AFFX-PheX-M_at 6.5
AFFX-PheX-3_at 6.5
AFFX-ThrX-5_at 6.5
AFFX-ThrX-M_at 6.5

Total number of rows: 8993

Table truncated, full table size 155 Kbytes.

Supplementary file Size Download File type/resource
GSM1080539_TOXO_RH-JSR.CEL.gz 947.0 Kb (ftp)(http) CEL
Processed data included within Sample table

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