|
Status |
Public on Aug 25, 2017 |
Title |
Schizont, alba4-null Replicate 2 |
Sample type |
SRA |
|
|
Source name |
Schizonts
|
Organism |
Plasmodium yoelii |
Characteristics |
strain: Py17XNL genotype: alba4-
|
Growth protocol |
Naïve female mice were infected with either WT-GFP or alba4-null parasites, and parasitemia was allowed to reach 1%. Schizonts and gametocytes were harvested from these mice. Naïve female mosquitoes were allowed to take a blood meal from mice infected with either WT-GFP or alba4-null parasites, and sporozoites were collected from the midguts ten days post-blood meal. Two million sporozoites were used per replicate per parasite line.
|
Extracted molecule |
total RNA |
Extraction protocol |
Following purification of the parasite samples, RNA from all sample types was isolated by the QIAgen RNeasy Kit using the manufacturer’s protocol with the additional on-column DNaseI digestion. RNA yields were quantified spectrophotometrically, and the quality of all samples was confirmed by measuring RNA Integrity Number (RIN) using the Agilent Bioanalzyer. A barcoded library was made from each sample by using the Illumina TruSeq Stranded mRNA Library Prep Kit according to the manufacturer's protocol. qPCR was performed to determine the concentration of each library and an equimolar pool was made of all libraries.
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|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2500 |
|
|
Description |
489_614_Schizont_ Cuffdiff.xlsx 614
|
Data processing |
The resulting data was mapped to the P. yoelii 17XNL strain reference genome (plasmodb.org, v27) using Tophat2 in a local Galaxy instance. Gene and transcript expression profiles for both WT and alba4-null assemblies were generated using Cufflinks (Galaxy version 2.2.1.0), merged into a separate large transcript assemblies with Cuffmerge (Galaxy version 2.2.1.0). Resulting assemblies were compared using Cuffdiff (Galaxy version 2.2.1.3). Differential transcript abundances were measured in fragments per kilobase of transcript per million mapped fragments (FPKM). All default parameters were used for this analysis, except that a masked file containing known non-coding RNAs was applied and the number of maximum fragments per locus allowed was increased from 50,000 to 1,000,000. For the purified schizont and gametocyte samples, three biological replicates were merged for WT and pyalba4- profiles. Oocyst sporozoite samples used two biological replicates for this analysis. Genome_build: PlasmoDB-28_Pyoeliiyoelii17X_Genome.fasta Supplementary_files_format_and_content: Excel files are the resulting CuffDiff output with FPKM values and statistics, taking into account the replicate datasets per life cycle stage.
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|
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Submission date |
May 24, 2016 |
Last update date |
May 15, 2019 |
Contact name |
Scott E. Lindner |
E-mail(s) |
Scott.Lindner@psu.edu
|
Phone |
8148674062
|
Organization name |
Penn State University
|
Department |
Biochemistry and Molecular Biology
|
Street address |
W224 Millennium Science Complex
|
City |
University Park |
State/province |
Pennsylvania |
ZIP/Postal code |
16802 |
Country |
USA |
|
|
Platform ID |
GPL21940 |
Series (1) |
GSE81834 |
Comparative Total RNA-seq between WT and alba4-null Plasmodium yoelii parasites |
|
Relations |
BioSample |
SAMN05171935 |
SRA |
SRX1798480 |