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| Status |
Public on Oct 17, 2019 |
| Title |
PfDis3-DD_R_rep1_RNA-seq |
| Sample type |
SRA |
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| Source name |
malaria at Ring
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| Organism |
Plasmodium falciparum |
| Characteristics |
developmental stage: Ring
genotype/variation: PfDis3-DD
host: Homo sapiens
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Red blood cells infected by highly synchronous parasites were collected by centrifugation and resuspended in trizol that could be stored in -80℃ for a long time. After centrifugation, the supernatant was saved and then RNA was extracted according to reagent specification of Direct-zol™ RNA MiniPrep (R2052). The integrality of RNA was validated by 2% agarose gel.
Construction library was performed based on KAPA Stranded mRNA-Seq Kit (KK8421).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
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| Data processing |
Low-quality and adaptor sequences were trimmed from the reads using cutadapt (v1.16) with parameters: -a AGATCGGAAGAGC -A AGATCGGAAGAGC --trim-n -m 75 -q 20,20.
Then, the reads were mapped to the Plasmodium falciparum 3D7 genome (Pf 3D7 v32, obtained from PlasmoDB) using Hisat2 strand-specific mode (v2.1.0) with parameters: --rna-strandness RF --dta --no-discordant --no-mixed --no-unal.
The Samtools (v1.9) was used to transfer the mapping results from sam format to position sorted bam format.
Mapped reads were subsequently assembled into transcripts guided by the PlasmoDB gff annotation files (Pf 3D7 v32) using featureCounts (v1.6.1) with parameters: -M -p -B -C for all; -s 2 for sense transcripts; -s 1 for antisense transcripts.
Genome_build: Pf 3D7 v32
Supplementary_files_format_and_content: The raw counts were calculated by featureCounts as described above.
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| Submission date |
Jul 01, 2019 |
| Last update date |
Oct 17, 2019 |
| Contact name |
meng liu |
| E-mail(s) |
1710949@tongji.edu.cn
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| Organization name |
TongJi University
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| Street address |
1239,SiPing Road
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| City |
shanghai |
| ZIP/Postal code |
20082 |
| Country |
China |
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| Platform ID |
GPL26835 |
| Series (2) |
| GSE133651 |
TRIBE uncovers the role of Dis3 in shaping the dynamic transcriptome in malaria parasites [RNA-seq] |
| GSE133654 |
TRIBE uncovers the role of Dis3 in shaping the dynamic transcriptome in malaria parasites |
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| Relations |
| BioSample |
SAMN12175160 |
| SRA |
SRX6386835 |
| 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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