|
| Status |
Public on Feb 02, 2022 |
| Title |
3D7_AP2-EXP2-KD(-)GlcN_S_RNA-seq, Rep3 |
| Sample type |
SRA |
| |
|
| Source name |
schizont (40–45 hpi)
|
| Organism |
Plasmodium falciparum |
| Characteristics |
tissue: whole body
developmental stage: schizont (40-45 hpi)
strain: Pf 3D7
genotype: AP2-EXP2-KD
host: Homo sapiens
|
| Treatment protocol |
Parasites were tightly synchronized to a 5-hour window by isolating schizonts over a 40% and 70% Percoll-sorbitol gradient followed by sorbitol treatment 5 hours post re-invasion. Synchronized ring-stage parasites were diluted at 0.5% parasitemia with 2% hematocrit and cultured in the presence or absence of 5 mM glucosamine.
|
| Growth protocol |
Parasites were cultured in fresh O-type human erythrocytes in complete RPMI 1640 medium (Gibco) with 0.5% Albumax I (Invitrogen) and a gas phase maintained under 5% CO2, 5% O2 and 90% N2 at 37°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Highly synchronous parasites were collected in TRIzol at the ring (10–15 hpi), trophozoite (25–30 hpi), and schizont (40–45 hpi) stages from the next cycle, respectively. Total RNA purification was conducted with the Direct-zol RNA Kit (Zymo Research).
Libraries were prepared for strand-specific RNA sequencing by poly(A) selection with the KAPA mRNA Capture Beads (KAPA Biosystems) first and then RNA fragmentation to a size of 300–400 nucleotides. Subsequent library preparation steps followed the protocol of the KAPA Stranded mRNA-Seq Kit Illumina platform (KAPA Biosystems, KK8421).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
Parasites were not treated with glucosamine (GlcN)
|
| Data processing |
To remove residual adapters and low-quality bases, sliding window trimming was performed on reads with Trimmomatic v0.39 using a window size of 4 and average quality of the window above 15. A minimum read length of 50 bp and average read quality above 20 were required after read clipping.
HISAT2 v2.2.1 was employed to align trimmed RNA-seq reads to the P. falciparum 3D7 reference genome (release 47) with the guide by the gene annotation, using default parameters except --max-intronlen 5000 --dta --rna-strandness RF.
StringTie v2.1.2 was used to count reads mapped to each gene.
Genome_build: Pf 3D7 v47
Supplementary_files_format_and_content: matrix table with raw gene counts for every gene and every sample
|
| |
|
| Submission date |
Jul 20, 2021 |
| Last update date |
Feb 03, 2022 |
| Contact name |
Mei Jiang |
| E-mail(s) |
gingerplum@hotmail.com
|
| Phone |
862165985138
|
| Organization name |
Tongji University
|
| Street address |
1239 Siping Road
|
| City |
Shanghai |
| State/province |
Shanghai |
| ZIP/Postal code |
200092 |
| Country |
China |
| |
|
| Platform ID |
GPL26835 |
| Series (2) |
| GSE180436 |
Roles of PfAP2-EXP2 in Plasmodium falciparum blood-stage development [RNA-seq] |
| GSE180438 |
Roles of PfAP2-EXP2 in Plasmodium falciparum blood-stage development |
|
| Relations |
| BioSample |
SAMN20322097 |
| SRA |
SRX11503857 |
