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Sample GSM3058809 Query DataSets for GSM3058809
Status Public on Mar 22, 2018
Title 6A-R_TP1ART_074038_Cycle1
Sample type RNA
 
Channel 1
Source name P. falciparum, 6A-R clone, exposed to 900 nM ART for 1hr
Organism Plasmodium falciparum
Characteristics sample type: In vitro culture (derived fromn 3D7 strain), harvested after 1hr of exposure to 900 nM ART (initiated at 10 HPI)
Treatment protocol Synchronized parasites were exposed to 900 nM ART for 4 hrs, starting from 10 HPI
Growth protocol Synchronized P. falciparum parasites were grown at 1% parasitemia, 2% hematocrit, and synchronized using 5% sorbitol treatment at 4 HPI
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from parasite cultures using TRIZol-Chloroform method as previously described in detail in Bozdech, Z., S. Mok & A. P. Gupta, (2013) DNA microarray-based genome-wide analyses of Plasmodium parasites. Methods in molecular biology 923: 189-211.
Label Cy5
Label protocol Equal amounts (4 µg) of sample cDNA and reference cDNA generated from a 3D7 reference strain were labelled with Cy5 and Cy3, respectively, for 4 hours. Labelled products were subsequently purified and hybridized on the microarray chip using the Agilent hybridization system.
 
Channel 2
Source name P. falciparum 3D7 RNA reference pool
Organism Plasmodium falciparum
Characteristics sample type: In vitro culture, asexual blood stage, laboratory strain 3D7, mixture of equal amounts of RNA harvested every 6 hours over the 48-hour parasite's intraerythrocytic life cycle
Treatment protocol Synchronized parasites were exposed to 900 nM ART for 4 hrs, starting from 10 HPI
Growth protocol Synchronized P. falciparum parasites were grown at 1% parasitemia, 2% hematocrit, and synchronized using 5% sorbitol treatment at 4 HPI
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from parasite cultures using TRIZol-Chloroform method as previously described in detail in Bozdech, Z., S. Mok & A. P. Gupta, (2013) DNA microarray-based genome-wide analyses of Plasmodium parasites. Methods in molecular biology 923: 189-211.
Label Cy3
Label protocol Equal amounts (4 µg) of sample cDNA and reference cDNA generated from a 3D7 reference strain were labelled with Cy5 and Cy3, respectively, for 4 hours. Labelled products were subsequently purified and hybridized on the microarray chip using the Agilent hybridization system.
 
 
Hybridization protocol Hybridizations were performed for 20 hours at 65°C in a rotating hybridization oven at 10rpm.
Scan protocol Microarray scanning was done using PowerScanner (Tecan, Austria) at 10uM resolution and with autogain PMT adjustments for both channels. Data was acquired using GenePix Pro v6.0 software (Axon Instruments, USA) as described in Mok, S., M. Imwong et al (2011) Artemisinin resistance in Plasmodium falciparum is associated with an altered temporal pattern of transcription. BMC Genomics 12: 391.
Data processing Features with flag>0 and with median foreground intensity greater than 1.5 fold median background intensity for either channel were accepted. Log2 ratios were background corrected using a normexp method, followed by loess normalization within arrays, and subsequently with quantile normalization between arrays. Post processing was performed using the Linear Models for Microarray (LIMMA) package for R.
 
Submission date Mar 21, 2018
Last update date Mar 22, 2018
Contact name Frances Maureen Casica Rocamora
E-mail(s) roca0001@e.ntu.edu.sg
Organization name Nanyang Technological University
Department School of Biological Sciences
Street address 60 Nanyang Drive Nanyang Technological University
City Singapore
State/province Singapore
ZIP/Postal code 637551
Country Singapore
 
Platform ID GPL11248
Series (1)
GSE112149 In vitro transcriptomic profiling of P. falciparum under 4 hr artemisinin challenge (900nM), from 10 HPI

Data table header descriptions
ID_REF
VALUE Background corrected, loess and quantile-normalized log2ratio values

Data table
ID_REF VALUE
ac11rRNA18s_0 -0.225496086
ac11rRNA18s_1 -0.323639937
ac11rRNA28s_0 0.017804796
ac11rRNA28s_1 0.028301503
ac11rRNA28s_2 0.023932227
ac11rRNA5.8s_0 0.282944089
ac11rRNAITS1_0 0.708129069
ac11rRNAITS2_0 0.717634881
ac13rRNA18s_0 -0.065317946
ac13rRNA18s_1 -0.025891386
ac13rRNA18s_2 -1.135723741
ac13rRNA28s_0 -0.186689258
ac13rRNA28s_1 -0.125348125
ac13rRNA5.8s_0 0.429159619
ac13rRNAITS1_0 0.71655759
ac13rRNAITS2_0 0.894998009
ac14rRNA.1-5s_0 -0.004552821
ac14rRNA.2-5s_0 -0.037538736
ac14rRNA.3-5s_0 -0.004476257
ac1rRNA18s_0 -0.174149331

Total number of rows: 11005

Table truncated, full table size 266 Kbytes.




Supplementary file Size Download File type/resource
GSM3058809_6A-R_TP1ART_074038_Cycle1.gpr.gz 1.2 Mb (ftp)(http) GPR
Processed data included within Sample table

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