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| Status |
Public on May 26, 2021 |
| Title |
Impact of sickle cell trait hemoglobin on the intraerythrocytic transcriptional program of Plasmodium falciparum |
| Organism |
Plasmodium falciparum |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Purpose: The goals of this study are to compare parasite transcriptomes in sickle cell trait infected red blood cells during the intraerythrocytic developmental cycle (IDC) from in vitro time series and in vivo blood samples to identify new therapeutic targets in the treatment of malaria
Methods: In vitro time series: Parasites were synchronized to early ring-stage parasites and sampled every three hours for 48 hours to capture every stage of the IDC, generating 16 RNA-seq libraries per replicate (128 total). In vivo blood samples: Samples were collected in an observational study of malaria in children in Kenieroba, Mali (ClinicalTrials.gov Identifier: NCT02645604). From children presenting with uncomplicated falciparum malaria, we selected all available samples from children with HbAS and matched each of these to a sample from a child with HbAA on: month of episode, parasite density, ethnic background, and, if possible, ABO blood type.
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| Overall design |
mRNA profiles of P. falciparum in HbAS iRBCs compared to HbAA
in vitro
3 hour time points
16 time points per replicate
8 replicates (4 HbAA, 4 HbAS)
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128 RNA-seq libraries
in vivo
16 HbAA
16 HbAS
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32 RNA-seq libraries
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| Contributor(s) |
Saelens JW, Petersen JE, Freedman E, Moseley R, Konaté D, Diakité SA, Traoré K, Vance N, Fairhurst RM, Diakite M, Haase SB, Taylor SM |
| Citation(s) |
34668757 |
| Submission date |
Dec 14, 2020 |
| Last update date |
Nov 10, 2021 |
| Contact name |
Steve Taylor |
| E-mail(s) |
steve.taylor@duke.edu
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| Organization name |
Duke University School of Medicine
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| Department |
Division of Infectious Diseases
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| Lab |
Taylor
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| Street address |
303 Research Dr
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| City |
Durham |
| State/province |
NC |
| ZIP/Postal code |
27710 |
| Country |
USA |
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| Platforms (1) |
| GPL26836 |
Illumina NovaSeq 6000 (Plasmodium falciparum) |
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| Samples (160)
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| Relations |
| BioProject |
PRJNA685106 |
| SRA |
SRP297870 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE163144_RAW.tar |
6.9 Mb |
(http)(custom) |
TAR (of CSV) |
| GSE163144_counts_vitro.csv.gz |
2.1 Mb |
(ftp)(http) |
CSV |
| GSE163144_counts_vivo.csv.gz |
255.3 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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