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| Status |
Public on May 08, 2015 |
| Title |
Deep, strand-specific, non-polyA-selected RNA sequencing of biological replicate Plasmodium falciparum blood stage time-courses |
| Organism |
Plasmodium falciparum |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
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| Summary |
The human malaria parasite Plasmodium falciparum has a complex and multi-stage life cycle that requires extensive immune escape, invasion of human liver and blood cells, and transmission through the female Anopholes mosquito. To date, the regulatory elements orchestrating these critical parasite processes remain largely unknown. However, there is mounting evidence across a broad range of species that intergenic long non-coding RNA (lncRNA) and antisense RNA can regulate chromatin state and gene expression. To pursue such functional roles for lncRNAs in P. falciparum, we performed deep, strand-specific RNA sequencing of fifteen non-polyA-selected blood stage samples, and assembled and characterized the properties of 660 intergenic lncRNAs, 474 antisense RNAs, and 1381 circular RNAs (circRNAs). We further validated the non-canonical splice junctions of seven P. falciparum circRNAs, an emerging class of non-coding RNA with regulatory potential and unexplored functional significance in P. falciparum. Our comprehensive analysis of P. falciparum lncRNAs indicates a functional role for these transcripts; P. falciparum intergenic lncRNAs and antisense RNAs are developmentally regulated in a similar periodic fashion to annotated transcripts, and sense-antisense pair expression is significantly anti-correlated. Notable outliers include intergenic lncRNAs that strongly peak in expression during parasite invasion, such as the telomere-associated lncRNA-TARE family, antisense transcripts that drop in expression during parasite invasion, and a highly correlated, multi-exonic, antisense counterpart to P. falciparum Gametocyte Developmental Protein 1 (PfGDV1). Taken together, our results present over two thousand P. falciparum intergenic lncRNA, antisense, and circRNA candidates and highlight promising P. falciparum lncRNAs for future investigation.
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| Overall design |
We harvested fifteen blood stage samples from two biological replicate time-courses. The first time-course comprised of eleven samples that finely map temporal changes during P. falciparum blood stage development. We harvested samples over 56 hours, at roughly 4-hour time intervals, from a tightly synchronized P. falciparum 3D7 parasite population. As the asexual blood stage is an approximately 48-hour cycle, this time-course allowed us to profile gene expression during RBC rupture and parasite invasion. The second time-course comprised of four samples harvested in synchronous P. falciparum 3D7 parasites approximately four hours before and after the ring to trophozoite and trophozoite to schizont morphological stage transitions, which occur during the blood stage at 24 hours post invasion (hpi) and 36 hpi, respectively.
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| Contributor(s) |
Broadbent K, Broadbent JC, Ribacke U, Wirth D, Rinn JL, Sabeti PC |
| Citation(s) |
26070627 |
| Submission date |
May 08, 2014 |
| Last update date |
Jul 31, 2019 |
| Contact name |
Kate Mariel Broadbent |
| E-mail(s) |
kbroadb@fas.harvard.edu
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| Organization name |
Harvard University
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| Department |
Systems Biology
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| Lab |
Pardis Sabeti
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| Street address |
FAS Center for Systems Biology Northwest Building, room 469 52 Oxford Street
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| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02138 |
| Country |
USA |
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| Platforms (1) |
| GPL16607 |
Illumina HiSeq 2000 (Plasmodium falciparum) |
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| Samples (15)
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| Relations |
| BioProject |
PRJNA246463 |
| SRA |
SRP041795 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE57439_LncRNA_Properties.xlsx.gz |
437.0 Kb |
(ftp)(http) |
XLSX |
| GSE57439_PlasmoDBv10_Expression_FPKMs.txt.gz |
360.5 Kb |
(ftp)(http) |
TXT |
| GSE57439_Significant_Features.xlsx.gz |
398.9 Kb |
(ftp)(http) |
XLSX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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