|
| Status |
Public on Jan 09, 2021 |
| Title |
singlecell_clone_3 |
| Sample type |
SRA |
| |
|
| Source name |
in vitro 3D7 strain culture
|
| Organism |
Plasmodium falciparum |
| Characteristics |
developmental stage: blood stage schizonts
strain: 3D7 subclone
|
| Growth protocol |
P. falciparum 3D7 strain and subclone was maintained in RPMI 1640 medium (Gibco) supplemented with Albumax I (Gibco) (0.25%), hypoxanthine (Sigma) (0.1 mM), Sodium bicarbonate (Sigma) (2 g/L), and gentamicin (Gibco) (50 μg/L) in 2 % haematocrit at 37 oC on shaker.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Single cells were FACS sorted into lysis buffer directly. Total cell lysate was used for reverse transcription and cDNA amplification.
Illumina Nextera XT kit was used for library preparation according to the manufacturer's intructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
B6_A3
|
| Data processing |
Standard Illumina pipeline was used for base calling and demultiplexing
Sequenced reads were trimmed for adapter, primer and low quality bases from 3'-ends
Trimmed reads then mapped to Plasmodium falciparum 3D7 genome (genedb version 3) using HiSAT2 (version 2.1.0) with parameters --min-intronlen 60 --max-intronlen 2500 --fr
Only uniquely mapped reads were extracted using samtools (version: 1.8) and raw count generated by bedtools (v2.27.1)
standard normalized count Fragments Per Kilobase of transcript per Million mapped reads (FPKM) except gene length in the formula is replaced with mapped length
Genome_build: Plasmodium falciparum 3D7 geneDB version 3
Supplementary_files_format_and_content: Comma-separated (.csv) file include FPKM values for all the samples in the matrix form
|
| |
|
| Submission date |
Jan 08, 2021 |
| Last update date |
Jan 10, 2021 |
| Contact name |
Zbynek Bozdech |
| E-mail(s) |
ZBozdech@ntu.edu.sg
|
| Organization name |
Nanyang Technological University
|
| Department |
School of Biological Sciences
|
| Lab |
ZB Lab
|
| Street address |
60 Nanyang Drive
|
| City |
Singapore |
| ZIP/Postal code |
637551 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL26836 |
| Series (1) |
| GSE164459 |
Single Cell RNA Sequencing Reveals Transcriptional Heterogeneity and Stochastic Gene Expression in Plasmodium falciparum Schizonts |
|
| Relations |
| BioSample |
SAMN17260972 |
| SRA |
SRX9807607 |
