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Sample GSM5685080 Query DataSets for GSM5685080
Status Public on Jan 31, 2022
Title NF54-rep2-T0
Sample type SRA
 
Source name NF54_T0
Organism Plasmodium falciparum
Characteristics strain: NF54
genotype: wildtype
disrupted gene id: n/a
drug treatment: no drug control
Treatment protocol Cultures of wildtype NF54 and pB- mutant pB104 were highly synchronous rings, then split equally into two control and two experiments T75 flasks each. T0 samples were harvested. All parasites were grown at the normal human body temperature (37C) to early ring-stage. Two flasks of were then exposed to 3-cycles growth of low-dose of each antimalarial drug (dihydroartemisin-DHA and Bortezomib-BTZ), while the remaining two flasks without any drug exposure. After the third cycles-growth (T1), RNA was harvested simultaneously from all conditions for RNAseq.
Growth protocol Parasite cultures were maintained according to standard methods with gassing (5% O2 and 5% CO2, nitrogen balanced) and 5% hematocrit (O+ blood; Interstate Blood Bank) in RPMI 1640 medium (Invitrogen) supplemented with 0.5% Albumax II (Invitrogen), 0.25% sodium bicarbonate, and maintained at 37°C.
Extracted molecule total RNA
Extraction protocol Parasites were separated from red blood cells via incubation with 0.015% saponin at room temperature for 5 min. Cultures were then pelleted and washed three times in 10 mL room temperature PBS. Samples were stored at − 80 °C in 1 mL TRIzol reagent (Fisher Scientific, Hampton, NH) until extraction. At RNA extraction, 200 μl of chloroform was added and samples were vortexed vigorously for 15 seconds, followed by incubation at room temperature for up to 5 minutes. Samples were then spun down at 12000×g (10,800 rpm) at 4 °C for 10 minutes and the supernatant discarded. 1 mL of 75% ethanol was added to the pellet, and samples were spun down at 10000×g (9800 rpm) for 5 minutes. The resulting supernatant was discarded and the pellet briefly allowed to dry. The RNA pellet was then dissolved in 20–50 μl of DEPC-treated water while being incubated at 55 °C for 10–15 min.
0.5 μg–1.0 μg of RNA samples were prepped for sequencing using the Illumina TruSeq Stranded mRNA Kit as per kit protocol. Library quantification was measured by qPCR and TapeStation (Agilent Technologies). Sequencing was performed on an Illumina NextSeq V2.5 mid-output 300-cycle.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Data processing RNAseq reads from each sample were aligned to the P. falciparum reference genome usinf HISAT2.
Mapped reads were used to assemble known transcripts from the reference and their abundances were estimated using SAMtools and the abundances were estimated using Feature Counts
Genome_build: P. falciparum reference genome (PlasmoDB version 47)
Supplementary_files_format_and_content: RNAseq_data_processed_counts.txt is the output of Fecture counts and contains ID (Geneid), chromosome (Chr),vcoordenadenades (Start and End), Strand (+ or -), Length and rhe counts (number of reads), for each mapped gene from each RNAseq sample.
 
Submission date Nov 10, 2021
Last update date Jan 31, 2022
Contact name Camilla Valente Pires
E-mail(s) camilla@usf.edu
Organization name University of South Florida
Street address 3720 Spectrum Blvd, 404
City TAMPA
ZIP/Postal code 33612
Country USA
 
Platform ID GPL21298
Series (1)
GSE188542 Antimalarial genetic screens of Plasmodium falciparum show peculiarities between the DHA and BTZ responses
Relations
BioSample SAMN23028998
SRA SRX13096947

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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