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Sample GSM956450 Query DataSets for GSM956450
Status Public on Jul 06, 2012
Title PF_gametocyte D8_delta PfPuf2_Rep3
Sample type RNA
 
Source name Plasmodium falciparum dalta PfPuf2, gametocyte stage III
Organism Plasmodium falciparum 3D7
Characteristics genotype/variation: delta-PfPuf2 mutant
developmental stage: Gametocyte Stage III
phenotype: higher ratio of male/female gametocyte
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)
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using the Trizol reagent ((invirtogen.com)
Label Cy3
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).
 
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.
Scan protocol Scanning was performed by Genomics Core Facility of Pennsylvania State University by using Axon GenePix 4000B.
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.
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).
 
Submission date Jul 05, 2012
Last update date Jul 06, 2012
Contact name JUN MIAO
E-mail(s) jmiao1@usf.edu
Phone 8139747374
Organization name University of South Florida
Department Internal Medicine
Lab Jun Miao and Liwang Cui
Street address 3720 Spectrum Boulevard, MDC84
City Tampa
State/province Florida
ZIP/Postal code 33612
Country USA
 
Platform ID GPL15768
Series (1)
GSE39124 Expression analysis of Plasmodium falciparum 3D7 delta-PfPuf2 mutant

Data table header descriptions
ID_REF
VALUE RMA-normalized, averaged gene-level signal intensity

Data table
ID_REF VALUE
MAL13P1.106100500001737 18634.41861
MAL13P1.114100500001750 187.2606786
MAL13P1.118100500001754 1069.687853
MAL13P1.119100500001755 4110.473808
MAL13P1.120100500001756 7370.789381
MAL13P1.121100500001759 4092.53813
MAL13P1.126100500001764 1682.480659
MAL13P1.129100500001768 12001.06817
MAL13P1.130100500001776 14141.75057
MAL13P1.131100500001780 486.9121763
MAL13P1.132100500001781 24735.00007
MAL13P1.133100500001782 10098.87862
MAL13P1.134100500001784 3233.661422
MAL13P1.135100500001786 682.6819694
MAL13P1.14100500001566 1838.65696
MAL13P1.146100500001831 582.5494731
MAL13P1.148100500001828 2141.096901
MAL13P1.150100500001822 1032.144634
MAL13P1.16100500001571 1603.450092
MAL13P1.160100500001838 413.5673878

Total number of rows: 5367

Table truncated, full table size 175 Kbytes.




Supplementary file Size Download File type/resource
GSM956450_416492A01_532.pair.gz 1.2 Mb (ftp)(http) PAIR
Processed data included within Sample table

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