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Status |
Public on Jul 06, 2012 |
Title |
PF_gametocyte D8_delta PfPuf2_Rep3 |
Sample type |
RNA |
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Source name |
Plasmodium falciparum dalta PfPuf2, gametocyte stage III
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Organism |
Plasmodium falciparum 3D7 |
Characteristics |
genotype/variation: delta-PfPuf2 mutant developmental stage: Gametocyte Stage III phenotype: higher ratio of male/female gametocyte
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Growth protocol |
P. falciparum clone 3D7 and dalta PfPuf2 mutant were maintained as described previously (Trager and Jensen, 1976) Induction of gametocytogenesis was performed as described (Fivelman et al., 2007). Ganetocytes were harvested at Day 8 (stage III) and Day 12 (stage V)
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Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was extracted using the Trizol reagent ((invirtogen.com)
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Label |
Cy3
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Label protocol |
Labeling was done by Genomics Core Facility of Pennsylvania State Univerity. Amplify 1ug of each sample using the Ambion (Life Technologies) Amino Allyl MessageAmp II aRNA Amplification Kit. Dye couple 15 ug of aRNA with Cy3 or Cy5 (GE Health Care #RPN5661), as appropriate, and subsequently purify according to the Ambion Kit instructions.(AM1753).
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Hybridization protocol |
Hybridization was performed by Genomics Core Facility of Pennsylvania State University. Incubate at 95C for 5 minutes, followed by 42C for 5 minutes. Attach appropriate mixer to the array and add hybridizations solution according to the manufacturer’s instructions (Roche NimbleGen). Hybridize with mixing in a MAUI hybridization instrument overnight at 42C.
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Scan protocol |
Scanning was performed by Genomics Core Facility of Pennsylvania State University by using Axon GenePix 4000B.
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Description |
This sample is of Plasmodium falciparum 3D7 with deletion of PfPuf2 at gametocyte stage III. It is the third of three mutant strain biological replicates used in this experiment, each from separate cultures.
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Data processing |
The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in DNASTAR software-ArrayStar 4 (dnastar.com).
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Submission date |
Jul 05, 2012 |
Last update date |
Jul 06, 2012 |
Contact name |
JUN MIAO |
E-mail(s) |
jmiao1@usf.edu
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Phone |
8139747374
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Organization name |
University of South Florida
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Department |
Internal Medicine
|
Lab |
Jun Miao and Liwang Cui
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Street address |
3720 Spectrum Boulevard, MDC84
|
City |
Tampa |
State/province |
Florida |
ZIP/Postal code |
33612 |
Country |
USA |
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Platform ID |
GPL15768 |
Series (1) |
GSE39124 |
Expression analysis of Plasmodium falciparum 3D7 delta-PfPuf2 mutant |
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