|
| Status |
Public on Feb 07, 2022 |
| Title |
BisRNA-seq_Pf_G1_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
BisRNA-seq_Pf_G1_rep2
|
| 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 |
The parasite pellets were washed twice with precooling 1 X PBS and then resuspended in 1 mL TRIzol (Invitrogen). Total RNA was extracted using the Direct-zol RNA Kit (Zymo Research) according to the manufacturer’s instructions. mRNA enrichment from the total RNA was performed using the Dynabeads™ mRNA Purification Kit (invitrogen) as per the manufacturer’s instructions.
RNA bisulfite treatment and purification of converted RNA was performed using the Methylamp™ RNA Bisulfite Conversion Kit (Epigentek Group Inc.) according to the manufacturer’s instructions. One ug mRNAs along with 5 ng Dhfr RNA (1:2000) as methylation conversion control were used and as input RNA. The converted RNA was subsequently used for fragmentation and library construction using the KAPA Stranded mRNA-Seq Kit (KAPA) according to the instructions provided by the manufacturer.
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| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Pf_G1_2
mRNA
m5C.Pf.txt
|
| Data processing |
Library strategy: RNA-BisSeq
Raw sequencing data were filtered to remove low-quality reads and adapter contaminations with cutadapt. Reads with average quality score >= 20 and length >=50bp were kept. Clean reads were mapped to the Plasmodium falciparum 3D7 genome (Pf 3D7 v32, obtained from PlasmoDB) or to the Plasmodium yoelii 17X genome (Py17x v45, obtained from PlasmoDB) using software meRanGs suit meRanGh align. Only unambiguously aligned reads were used to call m5C sites using meRanCall suit from meRanGh(40) (FDR < 0.01). Analysis of the Dhfr spike-in revealed C-T conversion around 98% (Dataset S1). Candidate cytosine positions were covered by at least 20 reads, methylated cytosine depth greater than 5 and m5C methylation level greater than 0.1. m5C sites detected in both two replicates were considered as valid m5C sites and used for further analysis.
Genome_build: Pf 3D7 v32 and Py17x v45
Supplementary_files_format_and_content: *.txt: Tab-delimited text files containing m5c level of genes at different stages in Plasmodium.
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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) |
| GSE159126 |
5-methylcytosine modification-mediated mRNA stabilization is associated with sexual development of malaria parasites [BisRNA-seq] |
| GSE159127 |
5-methylcytosine modification-mediated mRNA stabilization is associated with sexual development of malaria parasites |
|
| Relations |
| BioSample |
SAMN16380813 |
| SRA |
SRX9251219 |
