|
| Status |
Public on Jan 30, 2016 |
| Title |
Female 3-rRNA |
| Sample type |
SRA |
| |
|
| Source name |
Female gametocyte
|
| Organism |
Plasmodium falciparum |
| Characteristics |
strain: 3D7
tissue: Female
age: Day 12
tissue: gametocyte at stage V
|
| Growth protocol |
P. falciparum parasites were maintained as described previously (Trager and Jensen, 1976)
Induction of gametocytogenesis was performed as described (Fivelman et al., 2007). Ganetocytes were harvested at Day 12 (stage V).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The male and female gametocytes were separated by cell-sorter based on GFP intensity. Total RNA was extracted using the Trizol reagent (invirtogen.com)
Labeling was done by Genomics Core Facility of Pennsylvania State Univerity. Total RNA with and without rRNA depletion were processed for generation libraries using the Illumina TruSeq Stranded mRNA Library Preparation kit (Illumina Inc., San Diego, CA).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
This sample is of Plasmodium falciparum female gametocyte at stage V. It is the third of three biological replicates used in this experiment, each from separate cultures.
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mapped to the P. falciparum genome sequence (Genedb v3.1) using TopHat (Trapnell et al., 2009). Output was filtered to retain only reads that were mapped with ≤ 2 mismatches in the 100-bp long reads.
The RNA-Seq data were converted to transcripts levels by by Kallisto followed by Deseq (Anders and Huber, 2010; Bray et al., 2015). The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: P. falciparum genome sequence (Genedb v3.1)
Supplementary_files_format_and_content: Excel files include values for each genes from each samples
|
| |
|
| Submission date |
Jan 29, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
JUN MIAO |
| E-mail(s) |
jmiao1@usf.edu
|
| Phone |
8139747374
|
| Organization name |
University of South Florida
|
| Department |
Internal Medicine
|
| Lab |
Jun Miao and Liwang Cui
|
| Street address |
3720 Spectrum Boulevard, MDC84
|
| City |
Tampa |
| State/province |
Florida |
| ZIP/Postal code |
33612 |
| Country |
USA |
| |
|
| Platform ID |
GPL21078 |
| Series (1) |
| GSE77398 |
Next generation sequencing analysis of transcriptomes of Plasmodium falciparum male and female gametocytes |
|
| Relations |
| BioSample |
SAMN04448322 |
| SRA |
SRX1553674 |
