|
| Status |
Public on Feb 07, 2022 |
| Title |
RNA_seq_Pf_G2_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
RNA_seq_Pf_G2_rep1
|
| Organism |
Plasmodium falciparum |
| Characteristics |
strain: Pf NF54
genotype: Wild type
host: Human
developmental stage: Gametocyte
tissue: Whole body
|
| Treatment protocol |
Phenylhydrazine (80 μg/g mouse body weight) was used to treat with the ICR mouse through intraperitoneal injection; For P. falciparum, 50 mM N-acetyl-D-glucosamine was added to the cultures for three consecutive days to kill the asexual-stage parasites after sexual commitment. P. falciparum schizont-stage parasite cultures were synchronized by repeated sorbitol and percoll-sorbitol treatments (Lambros and Vanderberg, 1979).
|
| Growth protocol |
P. falciparum parasite-infected red blood cells were cultured in T75 flask at 2% hematocrit in the presence of 5% O2 and 5% CO2 (rest N2) in RPMI 1640 supplemented with 25mM Hepes, 50mg/l Hypoxanthine, 0.21% NaHCO3, 0.5% Albumax I and 20mg/l Gentamicin; P. yoelii parasite-infected ICR mice (female, 5 to 6 weeks old) were housed in the Animal Care Center of Xiamen University and kept at room temperature under a 12 h light/dark cycle at a constant relative humidity of 45%.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Parasites were harvested and total RNA was isolated using TRIzol (Life) according to the manufacturer’s manual and further purified using the Direct-zol RNA Kit (ZYMO RESEARCH) for removal of gDNA. Residual gDNA was digested with TURBO DNA-freeTM DNaseI (Ambion) and the RNA was quantified by NanoDrop.
The poly(A) RNA isolation, mRNA enrichment and library construction were performed as described using 15 cycles of library amplification. The mRNA was enriched by poly(A) selection with the KAPA mRNA Capture Beads (KAPA), and fragmented to about 300–400 nucleotides (nt) in length, then all subsequent steps were performed in accordance with an KAPA Stranded mRNA-Seq Kit Illumina platform (KAPABIOSYSTEMS KK8421-96 libraries).
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| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Pf_G2_1
mRNA
Fpkm.Pf.txt
|
| Data processing |
Low-quality and adaptor sequences were trimmed using cutadapt (v1.18)(42) with parameters: -a AGATCGGAAGAGC -A AGATCGGAAGAGC --trim-n -m 50 -q 20,20. RNA sequencing reads were aligned using hisat2 (v2.1.0)(43) with strand specific mode (--rna-strandness RF) to the Plasmodium falciparum 3D7 genome (Pf 3D7 v32, obtained from PlasmoDB) or to the Plasmodium yoelii 17X genome (Py17x v45, obtained from PlasmoDB). Mapped reads were subsequently assembled into transcripts guided by the PlasmoDB gff annotation files (Pf3D7 v32/ Py17x v45) using featureCounts (v1.6.1)(44) with parameters: -M -p -B -C -s 2. Read counts were obtained using featureCounts (v1.6.1).
Genome_build: Pf 3D7 v32 and Py17x v45
Supplementary_files_format_and_content: *.txt: Tab-delimited text files for gene expression.
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| |
|
| Submission date |
Oct 06, 2020 |
| Last update date |
Feb 07, 2022 |
| Contact name |
meng liu |
| E-mail(s) |
1710949@tongji.edu.cn
|
| Organization name |
TongJi University
|
| Street address |
1239,SiPing Road
|
| City |
shanghai |
| ZIP/Postal code |
20082 |
| Country |
China |
| |
|
| Platform ID |
GPL26836 |
| Series (2) |
| GSE159124 |
5-methylcytosine modification-mediated mRNA stabilization is associated with sexual development of malaria parasites [RNA-seq] |
| GSE159127 |
5-methylcytosine modification-mediated mRNA stabilization is associated with sexual development of malaria parasites |
|
| Relations |
| BioSample |
SAMN16380754 |
| SRA |
SRX9251198 |
