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Status |
Public on Oct 31, 2021 |
Title |
02-017 |
Sample type |
SRA |
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Source name |
parasites isolates
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Organism |
Plasmodium falciparum |
Characteristics |
clinical presentation: cerebral malaria
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Extracted molecule |
polyA RNA |
Extraction protocol |
RNA was extracted as described in Ponts N et al 2012, then digested with DNAse I (Qiagen) and purified using RNEasy MinElute Cleanup kit column (Qiagen). Absence of genomic DNA was assessed by the absence of amplification of p90 gene in qPCR from the direct use of the RNA extract, using Syber Green reagent (Life Technology) on Rotorgene 6000. RNA quality was assessed using Nanodrop (2000c) dosage and Agilent RNA 6000 Pico Kit used with 2100TM Bioanalyzeur (Agilent). RNA-seq libraries were performed by TruSeq Stranded mRNA protocol (Illumina®, California, U.S.A.)
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
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Description |
D349T39
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Data processing |
Mapping with Hisat2 2.2 Aligned reads were assigned to annotated features with Feature-counts 2.0.1 Genome_build: P.falciparum 3D7, PlasmoDB release 49 Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene except for variant surface antigens and every sample
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Submission date |
Oct 29, 2021 |
Last update date |
Oct 31, 2021 |
Contact name |
Gwladys Bertin |
E-mail(s) |
gwladys.bertin@ird.fr
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Organization name |
Institut de Recherche pour le Développement
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Street address |
rue de l'observatoire
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City |
Paris |
ZIP/Postal code |
75006 |
Country |
France |
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Platform ID |
GPL26836 |
Series (1) |
GSE186820 |
Transcriptome analysis of Plasmodium falciparum isolates from Benin reveals specific gene expression associated with cerebral malaria |
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Relations |
BioSample |
SAMN22782170 |
SRA |
SRX12836755 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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