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Sample GSM4224241 Query DataSets for GSM4224241
Status Public on Aug 31, 2021
Title PfNot1.2 knockdown, TP1, replicate 1
Sample type RNA
 
Channel 1
Source name P. falciparum T996 RNA, PfNot1.2 knockdown
Organism Plasmodium falciparum
Characteristics culture, stage, strain, harvest timepoint, estimated developmental age: In vitro culture, asexual blood stage, laboratory strain T996, TP1, 4 hpi
Treatment protocol Selective drugs were removed from medium two intraerythrocytic life cycles before harvesting parasites for RNA extraction.
Growth protocol P. falciparum parasites were cultured in RPMI-HEPES medium , supplemented with 0.25% Albumax , 0.2% sodium bicarbonate, 100 µM hypoxanthine and 10 µg/ml Gentamycin with 2% hematocrit.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using Trizol following manufacturer's instructions and as described 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 Synthesis of aminoallyl-coupled cDNA by reverse transcription and labeling of samples with cy fluorophore were carried out as described 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.
 
Channel 2
Source name P. falciparum 3D7 RNA reference pool
Organism Plasmodium falciparum
Characteristics culture, stage, strain, composition: In vitro culture, asexual blood stage, laboratory strain T996, mixture of equal amounts of RNA harvested every 8 hours over the 48-hour parasite's intraerythrocytic life cycle
Treatment protocol Selective drugs were removed from medium two intraerythrocytic life cycles before harvesting parasites for RNA extraction.
Growth protocol P. falciparum parasites were cultured in RPMI-HEPES medium , supplemented with 0.25% Albumax , 0.2% sodium bicarbonate, 100 µM hypoxanthine and 10 µg/ml Gentamycin with 2% hematocrit.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using Trizol following manufacturer's instructions and as described 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 Synthesis of aminoallyl-coupled cDNA by reverse transcription and labeling of samples with cy fluorophore were carried out as described 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.
 
 
Hybridization protocol Equal amounts of labelled sample and reference cDNA were hybridized on the microarray chip using the Agilent hybridization system. 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.
Description 104071_Cycle2_2018-02-09_KD_TP1_rep1
Transcriptional profiling of the PfNot1.2 knockdown line at Timepoint 1 at around 4 hpi, replicate 1
Data processing Features with flag>0 and with median foreground intensity greater than 1.5 fold median background intensity for either channel passed quality control and were accepted. Local background correction using normexp, followed by lowess normalization across all features were carried out to generate the normalized Log2 gene expression ratios.
 
Submission date Dec 18, 2019
Last update date Aug 31, 2021
Contact name Ying Liu
E-mail(s) yliu037@e.ntu.edu.sg
Phone 84030462
Organization name Nanyang Technological University
Department School of Biological Sciences
Lab Prof. Zbynek Bozdech's lab
Street address 60 Nanyang Drive
City Singapore
ZIP/Postal code 637551
Country Singapore
 
Platform ID GPL11248
Series (1)
GSE142275 Transcriptional profilling of Plasmodium falciparum parasites with disrupted PfNot1.1 (PF3D7_1103800) or PfNot1.2 (PF3D7_1417200)

Data table header descriptions
ID_REF
VALUE Background corrected and lowess normalized log2 transformed ratios (Cy5/Cy3) of the RNA sample/3D7 RNA reference pool.

Data table
ID_REF VALUE
ac11rRNA18s_0 0.016170981
ac11rRNA18s_1 0
ac11rRNA28s_0 -0.01887257
ac11rRNA28s_1 -0.136471077
ac11rRNA28s_2 0.005185513
ac11rRNA5.8s_0 -0.21590647
ac11rRNAITS1_0 0.072409495
ac11rRNAITS2_0 -0.056320784
ac13rRNA18s_0 -0.010655004
ac13rRNA18s_1 -0.555163447
ac13rRNA18s_2 0.012148633
ac13rRNA28s_0 -0.04036192
ac13rRNA28s_1 0.00850125
ac13rRNA5.8s_0 -0.472471011
ac13rRNAITS1_0 0.066427243
ac13rRNAITS2_0 null
ac14rRNA.1-5s_0 0
ac14rRNA.2-5s_0 -0.01179044
ac14rRNA.3-5s_0 -0.013733985
ac1rRNA18s_0 0.023198859

Total number of rows: 11005

Table truncated, full table size 268 Kbytes.




Supplementary file Size Download File type/resource
GSM4224241_104071_Cycle2_2018-02-09_KD_TP1_rep1.gpr.gz 1.2 Mb (ftp)(http) GPR
Processed data included within Sample table

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