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Sample GSM2086463 Query DataSets for GSM2086463
Status Public on Mar 22, 2016
Title RNA-Troph_2
Sample type SRA
 
Source name P. falciparum in vitro culture
Organism Plasmodium falciparum
Characteristics strain: PfBDP1HA
tissue: whole organism
Stage: Troph
Growth protocol Plasmodium falciparum parasites were cultured in RPMI-HEPES medium containing 5% O+ red blood cells, 0.2% sodium bicarbonate and 0.5% Albumax (Gibco). Parasitaemia was maintained at 0.5%-10%. Parasites cultures were incubated at 37ºC in 1% O2, 5% CO2 and 94% N2.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using Trizol (Life Technologies) following manufacturer's instructions
2 ug total RNA was depleted of Hb mRNA (GLOBINclear kit, Life Technologies) and other mRNAs purified using magnetic oligo dT beads. Indexed sequencing libraries were prepared using the NEBNext Ultra directional RNAseq kit (New England Biolabs). The PCR Library Enrichment step was replaced by a custom PCR protocol using the KAPA Hifi PCR system (KAPA Biosystems) for 12 cycles (Oyola et al., 2012).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description BDP1_T_cat_genes.fpkm_tracking.txt
Data processing All Samples were quality controlled using FastQC (version 0.11.2, http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Adapter sequences were trimmed and reads were quality filtered using Trim Galore! (version 0.3.7, www.bioinformatics.babraham.ac.uk/projects/trim_galore/)
ChIPseq: Sequence reads from ChIP and input samples were then mapped to the P. falciparum 3D7 strain genome assembly (PlasmoDB v12) using Subread (Liao et al., 2013)
Peaks were called using MACS2 q=0.01 (Zhang et al., 2008) using Bam files concatenated with Samtools (Li et al., 2009) from three biological replicates for schizonts and two for trophozoites for both ChIPseq and input libraries as per Zhang et al’s instructions (Zhang et al., 2008).
Genes closest to a ChIP peak were identified using the bedtools suite (Quinlan and Hall, 2010).
RNAseq: Sequence reads from RNASeq were mapped to the P. falciparum 3D7 strain genome assembly using Tophat2
The gene annotations are publicly available in the Plasmodium database PlasmoDB (http://plasmodb.org/plasmo/)
Transcript coverage normalised for gene and library size (fpkm) was determined using Cufflinks (Trapnell et al., 2012).
Genome_build: PlasmoDB v12
Supplementary_files_format_and_content: tab-delimited text files include FPKM (fragments per kilobase of exon per million fragments mapped) values for concatenated data sets
Supplementary_files_format_and_content: xls files include ChIP peaks called for concatenated data sets
 
Submission date Mar 11, 2016
Last update date May 15, 2019
Contact name Michaela Petter
E-mail(s) mpetter@unimelb.edu.au
Organization name University of Melbourne
Department Peter Doherty Institute
Street address 792 Elizabeth Street
City Melbourne
State/province VIC
ZIP/Postal code 3000
Country Australia
 
Platform ID GPL21078
Series (2)
GSE64691 A Novel Plasmodium Falciparum Bromodomain Protein Regulates Invasion Gene Expression
GSE79135 Genome-wide localisation of the bromodomain protein PfBDP1 in the malaria parasite P. falciparum
Relations
BioSample SAMN04571830
SRA SRX1651609

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

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