Dataset features

Specifications


Application: Gene expression microarray analysis
Number of samples: 32
Release date: Dec 13 2016
Last update date: Nov 20 2018
Access: Public
Diseases: Malaria, Malaria, Falciparum
Chemicals: Calcium
Dataset link Global transcriptomic changes of either cell cycle arrested parasites or cell cycle re-entered asexual P. falciparum 3D7 parasites.

Experimental Protocol


Two sets of independent oligonucleotide DNA microarrays were performed to analyze the global transcriptomic changes P. falciparum parasites using either DFMO-arrested parasites or DFMO-arrested parasites followed by putrescine-reversal. DNA microarrays were performed using custom microarray slides that contained 12 468 oligos (60-mer, Agilent Technologies) based on the complete P. falciparum genome. Synchronized ring-stage parasitized erythrocytes (5% hematocrit, 10-15% parasitemia) were incubated with DFMO (IC90) at 37˚C prior to sampling (Arrested time points: A1=21 h post treatment (hpt); A2=29 hpt) or additionally treated after 24 h DFMO pressure with 2 mM putrescine dihydrochloride to induce the re-entry and onset of the cell cycle (Re-entry time points: Re1=27 hpt; Re2=30 hpt and Re3=36 hpt). For each time point, two biological repeats were performed, each with two technical repeats. From 50 ml parasite cultures sourced at specific time points, RNA isolation, cDNA synthesis and dye coupling with Cy3 (reference pool) or Cy5 (samples) were performed as described in van Brummelen, A. C. et al. The Journal of biological chemistry 284, 4635-4646, doi:10.1074/jbc.M807085200 (2009). The slides were scanned using a GenePix™ 4000B scanner.

Repositories


GEO

GSE92289

BioProject

PRJNA357102

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Contact


LynMarie Birkholtz