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Sample GSM5404649 Query DataSets for GSM5404649
Status Public on May 25, 2022
Title P. falciparum drug-resistant line — MRA_1236 (RNA Replicate 2)
Sample type SRA
 
Source name P. falciparum blood-stage cultures
Organism Plasmodium falciparum
Characteristics strain: IPC 3445 (MRA_1236)
type: drug-resistant
Stage: Early trophozoite
Growth protocol Parasites were cultured in RPMI1640 medium supplemented with 25 mM HEPES, 0.5 % AlbuMAX I, 1.77 mM sodium bicarbonate, 100 μM hypoxanthine and 12.5 μg ml−1 gentamicin sulfate at 37 °C; subculture every two days; parasitemia maintained at ~5%
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using TRIzol reagent according to the protocol. DNAse treated RNA was used for cDNA synthesis
The cDNA libraries were prepared for samples using Illumina TruSeq RNA library preparation kit
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model NextSeq 550
 
Description -
Data processing Alignment to reference genome using STAR aligner in basic 2-pass mode
Variant-calling using REDItools 2.0 (https://github.com/tizianoflati/reditools2.0) on aligned (BAM) files
Annotation with corresponding variant data from whole-genome sequencing followed by variant filtering
Deduplication of BAM files at filtered variant positions using samtools
Second round of variant-calling using REDItools 2.0
Genome_build: Plasmodium falciparum 3D7 v.41 (ASM276v2)
Supplementary_files_format_and_content: .res files (tab-separated text file containing variants from second round of variant calling) and .sf files (output files of gene abundance estimation using Salmon)
 
Submission date Jun 28, 2021
Last update date May 25, 2022
Contact name Krishanpal Karmodiya
E-mail(s) krish@iiserpune.ac.in
Organization name Indian Institute of Science Education and Research
Department Center of Excellence in Epigenetics
Street address Dr. Homi Bhabha Road
City Pune
State/province Maharashtra
ZIP/Postal code 411008
Country India
 
Platform ID GPL26920
Series (1)
GSE179055 Exceptionally high sequence-level variation in the transcriptome of Plasmodium falciparum
Relations
BioSample SAMN19921374
SRA SRX11243881

Supplementary file Size Download File type/resource
GSM5404649_1236_Rep2_quant.sf.gz 87.2 Kb (ftp)(http) SF
GSM5404649_1236r2_dedup.res.txt.gz 330.0 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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