|
| Status |
Public on Aug 22, 2018 |
| Title |
sc.iRBC.53 |
| Sample type |
SRA |
| |
|
| Source name |
single.P.falciparum.iRBCs
|
| Organism |
Plasmodium falciparum |
| Characteristics |
strain: 3D7-164_tdT
blood_group: A
sampling_timepoint: T4
library quality: high
group: single-cell
sub-population: SP.1
batch: two
|
| Extracted molecule |
total RNA |
| Extraction protocol |
SmartSeq2 (Picelli S, Nat Methods. 2013, PubMed PMID: 24056875)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Aligned reads with STAR version 2.3 to combined genomes of P.falciparum(Pf3D7v3) and human (hg19) with the outSAMstrandField set to 'intronMotif'.
Calculated expression values with rpkmforgenes.py (available at https://github.com/danielramskold/S3_species-specific_sequencing) with options -readcount -fulltranscript -mRNAnorm -rmnameoverlap -bothendceil and gene annotation for the UCSC genome browser Ensembl track and Plasmodb release 11.1 annotation for P.falciparum (Pf3D7v3).
Principal component analysis done using prcomp function and t-stochastic neighbour embedding performed using tsne version 0.1-3 in R.
Single-cell differential expression analysis done using SCDE version 2.8.0.
Genome_build: Combined Pf3D7v3 (Plasmodb release 11.1) and hg19 (UCSF Human Genome Assembly)
Supplementary_files_format_and_content: Tab-delimited text with each row and column corresponding to P. falciparum genes and samples respectively. The first 208 fields represent the read counts and the next 208 are the normalized gene expression measurements (RPKM).
|
| |
|
| Submission date |
Jun 27, 2018 |
| Last update date |
Aug 22, 2018 |
| Contact name |
Rickard Sandberg |
| Organization name |
Karolinska Institutet
|
| Department |
Cell and Molecular Biology
|
| Lab |
Sandberg Lab
|
| Street address |
Solnavägen 9 Solna
|
| City |
Stockholm |
| ZIP/Postal code |
17165 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL16607 |
| Series (1) |
| GSE116341 |
Exploring parasite heterogeneity using single-cell RNA-seq reveals a gene signature among sexual stage Plasmodium falciparum (P.falciparum) parasites |
|
| Relations |
| BioSample |
SAMN09501557 |
| SRA |
SRX4313042 |
