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Series GSE66669 Query DataSets for GSE66669
Status Public on Oct 01, 2015
Title Plasmodium falciparum whole-genome real-time transcription and decay
Organism Plasmodium falciparum
Experiment type Expression profiling by array
Other
Summary To date, total mRNA analysis throughout intraerythrocytic development of the malaria parasite, Plasmodium falciparum, has only revealed abundance profiles of each gene at a given time. Here, we reveal that biosynthetic pyrimidine labeling allows for the calculation of real-time, whole-genome analysis of transcription and stability throughout asexual development. In turn, we are now able to determine transcriptional and decay rates at any given time during development of specific genes or subsets of genes which will drive new investigations on both transcriptional and post-transcriptional regulatory dynaimc and networks.
 
Overall design A single timecourse experiment in which 48 individual cultures were highly synchronized and, at a given hour post invasion (0-47), were treated with 40um 4-TU for 10min followed immediately by Trizol total RNA extraction. Total RNA from each timepoint was then biotinylated via a thiol-group on any transcript that incorporated a modified UTP. Streptavidin modified transcripts were then separated from total RNA by Streptavidin magentic beads resulting in a Labeled sample. Any mRNA that was not bound to the beads resulted in an Unlabeled sample. A fraction of the total RNA was untreated and resulted in a Total sample. Each hour, three samples were analyzed by microarray, Total, Unlabeled, and Labeled, resulting in 144 individual microarrays (48 for each sample type).
 
Contributor(s) Painter HJ, Chung NC, Storey JD, Llinás M
Citation(s) 29985403
Submission date Mar 09, 2015
Last update date May 15, 2019
Contact name Heather J Painter
Phone 8148673527
Organization name Penn State University
Department Molecular Biology & Biochemistry
Lab Manuel Llinas
Street address Millennium Science Center
City University Park
State/province Pennsylvania
ZIP/Postal code 16802
Country USA
 
Platforms (1)
GPL15130 Agilent-037237 P.falciparum_Pf3D7v7.1_Transcriptome_apimito
Samples (144)
GSM1627532 0hpi Total
GSM1627533 1hpi Total
GSM1627534 2hpi Total
Relations
BioProject PRJNA277701

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE66669_RAW.tar 678.6 Mb (http)(custom) TAR (of TXT)
Raw data provided as supplementary file
Processed data included within Sample table

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