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| Status |
Public on Oct 26, 2022 |
| Title |
Long-read transcriptomic sequencing of Plasmodium falciparum malaria parasite reveals isoforms with alternative 5′ ends |
| Organism |
Plasmodium falciparum 3D7 |
| Experiment type |
Other
|
| Summary |
The Plasmodium falciparum human malaria parasite genome is incompletely annotated and does not accurately represent the transcriptomic diversity of this species. To address this need, we performed long-read transcriptomic sequencing. To increase representation of mRNA isoforms expressed during intraerythrocytic stages, RNA was extracted from samples taken at time-points from synchronized cultures. 5 capped mRNA was enriched and converted to cDNA library. The cDNA libraries were sequenced on Nanopore and PacBio long-read platforms. Candidate non-redundant isoforms were annotated from each library dataset for creating a new transcript annotation catalog. Isoforms with alternative 5 ends represented the largest class of novel isoforms, although the majority of these do not seem to represent the products of alternative transcription initiation events. We suggest that most isoforms do not encode protein isoforms and instead represent RNA decay products.
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| Overall design |
Isoform profiles in ring, trophozoite and schizont stages of P. falciparum intraerythrocytic development obtained from total RNA and nuclear RNA samples
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| Contributor(s) |
Shaw PJ, Kaewprommal P, Wongsombat C, Tongsima S, Kamchonwongpaisan S, Piriyapongsa J |
| Citation(s) |
36331983 |
| |
| Submission date |
Oct 19, 2021 |
| Last update date |
Jan 26, 2023 |
| Contact name |
Pavita Kaewprommal |
| E-mail(s) |
pavita.kae@nstda.or.th
|
| Organization name |
NSTDA
|
| Department |
NBT
|
| Lab |
DATA
|
| Street address |
113
|
| City |
Khlong Nung |
| State/province |
Pathum Thani |
| ZIP/Postal code |
12120 |
| Country |
Thailand |
| |
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| Platforms (2) |
| GPL30880 |
Sequel (Plasmodium falciparum 3D7) |
| GPL32010 |
MinION (Plasmodium falciparum 3D7) |
|
| Samples (8)
|
| GSM5632411 |
Ring parasites nuclear fraction |
| GSM5632412 |
Trophozoite parasites nuclear fraction |
| GSM5632413 |
Schizont parasites nuclear fraction |
| GSM5632414 |
Combined Schizont and Trophozoite cytoplasmic fraction |
| GSM5929209 |
Mixed intraerythrocytic stage total RNA |
|
| Relations |
| BioProject |
PRJNA772676 |
| SRA |
SRP342074 |
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