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| Status |
Public on May 15, 2023 |
| Title |
Genomic adaptation underlies nutrient-driven reprogramming in malaria parasite [tRNA-Seq time series] |
| Organism |
Plasmodium falciparum |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
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| Summary |
We aimed to simultaneously characterize the dynamics of the codon and anti-codon pools during the intraerythrocytic developmental cycle
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| Overall design |
TGIRT-tRNAseq was performed on rings, trophozoites and schizonts with 3 replicates each, the anti-codon composition in the samples were then estimated from the read counts, charged level of each tRNA was estimated from a separate library with RNA pretreated with 50mM sodium periodate, pH4.8
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| Contributor(s) |
Chan SC, Li Q |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
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| Submission date |
Mar 03, 2023 |
| Last update date |
May 16, 2023 |
| Contact name |
Sherwin Chan |
| E-mail(s) |
sherwin.chan@ki.se
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| Organization name |
Karolinska Institutet
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| Street address |
Solnavagen 9
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| City |
Stockholm |
| ZIP/Postal code |
17177 |
| Country |
Sweden |
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| Platforms (1) |
| GPL26920 |
NextSeq 550 (Plasmodium falciparum) |
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| Samples (18)
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| GSM7080565 |
NF54 - ring, rep2 |
| GSM7080566 |
NF54 - Trophozoites, rep2 |
| GSM7080567 |
NF54 - Schizonts, rep2 |
| GSM7080568 |
NF54 - ring, rep3 |
| GSM7080569 |
NF54 - Trophozoites, rep3 |
| GSM7080570 |
NF54 - Schizonts, rep3 |
| GSM7080571 |
NF54 - ring, rep1, periodate treated |
| GSM7080572 |
NF54 - Trophozoites, rep1, periodate treated |
| GSM7080573 |
NF54 - Schizonts, rep1, periodate treated |
| GSM7080574 |
NF54 - ring, rep2, periodate treated |
| GSM7080575 |
NF54 - Trophozoites, rep2, periodate treated |
| GSM7080576 |
NF54 - Schizonts, rep2, periodate treated |
| GSM7080577 |
NF54 - ring, rep3, periodate treated |
| GSM7080578 |
NF54 - Trophozoites, rep3, periodate treated |
| GSM7080579 |
NF54 - Schizonts, rep3, periodate treated |
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| This SubSeries is part of SuperSeries: |
| GSE226632 |
tRNA regulation and amino acid usage bias reflect a coordinated metabolic adaptation in Plasmodium falciparum |
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| Relations |
| BioProject |
PRJNA940841 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE226631_RAW.tar |
40.0 Kb |
(http)(custom) |
TAR (of TXT) |
| GSE226631_tRNA_combined_AAAAA_api_and_human_A_to_I_tyr_intron_A2I.txt.gz |
5.4 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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