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Sample GSM2176444 Query DataSets for GSM2176444
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.
 
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.
 
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

Supplementary data files not provided
SRA Run SelectorHelp
Processed data are available on Series record
Raw data are available in SRA

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