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Sample GSM288485 Query DataSets for GSM288485
Status Public on May 22, 2008
Title Strain S27 Tachyzoite
Sample type mixed
Channel 1
Source name Tachyzoites
Organism Toxoplasma gondii
Characteristics 24 h in vitro tachyzoite
Treatment protocol None
Growth protocol Tachyzoites were grown in human foreskin fibroblasts in the presence of 10% serum in DMEM. Cells were infected at an MOI of 10 tachyzoites per cell and growth was carried out for 24h
Extracted molecule total RNA
Extraction protocol Total RNA was extracted with Trizol using the manufacturers instruction. mRNA was isolated from total RNA using the oligotex mRNA isolation kit (Qiagen)
Label Cy5
Label protocol cDNA was synthesized from mRNA using oligo-dT priming and reverse transcription. cDNA was then labeled with Cy5-dUTP using klenow (exo minus) and random primers
Channel 2
Source name empty pBluescript vector, in vitro transcribed
Organism synthetic construct
Characteristics common reference (in vitro transcribed RNA)
Treatment protocol None
Growth protocol Vector was propagated in DH5alpha cells.
Extracted molecule other
Extraction protocol Plasmid was isolated using Qiagen miniprep kit.
Label Cy3
Label protocol The polylinker region of the isolated plasmid was PCR-amplified using T3 and T7 primers. The PCR product was gel-purified using a Qiagen gel purification kit, and used as a template for in vitro transcription. The polylinker was transcribed in the presence of dUTP using the T7 RNA polymerase transcription kit (Maxiscript; Ambion).
Hybridization protocol Labeled cDNA was applied to array slides, covered with a coverslip, and hybridized at 68 degrees for 16-20 h. Slide were washed sequentially in 2X SSC, 1X SSC, and 0.5X SSC for 5 min each.
Scan protocol Slides were scanned on a GenePix scanner
Description PDS X CTG F1 Progeny clone S27
Data processing log2 ratios were normalized to a mean of 0 for all slides
Submission date May 14, 2008
Last update date May 20, 2008
Contact name Jon Boyle
Organization name Stanford University School of Medicine
Department Microbiology and Immunology
Lab Boothroyd Lab
Street address 299 Campus Drive
City Stanford
State/province CA
ZIP/Postal code 92305
Country USA
Platform ID GPL6851
Series (2)
GSE11437 Expression QTL mapping of Toxoplasma gondii genes, Bradyzoite array
GSE11515 Expression QTL mapping of Toxoplasma gondii genes

Data table header descriptions
VALUE log2 ratio (Cy5/Cy3)

Data table
251102 1.47
251103 0.63
251106 1.28
251107 2.19
251109 2.43
251110 2.17
251114 -0.66
251116 1.12
251119 -1.08
251121 0.47
251126 -1.08
251128 0.58
251132 0.26
251133 -2.6
251134 -2.28
251140 0.69
251141 0.94
251142 1.77
251143 0.74
251147 0.52

Total number of rows: 4403

Table truncated, full table size 53 Kbytes.

Supplementary file Size Download File type/resource
GSM288485.gpr.gz 1.2 Mb (ftp)(http) GPR
Processed data included within Sample table

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