|
| 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 |
