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Sample GSM5661595

Query DataSets for GSM5661595

Status

Public on Oct 31, 2021

Title

02-002

Sample type

SRA

Source name

parasites isolates

Organism

Plasmodium falciparum

Characteristics

clinical presentation: cerebral malaria

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.)

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina NovaSeq 6000

Description

D349T35

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

Submission date

Oct 29, 2021

Last update date

Oct 31, 2021

Contact name

Gwladys Bertin

E-mail(s)

gwladys.bertin@ird.fr

Organization name

Institut de Recherche pour le Développement

Street address

rue de l'observatoire