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| Status |
Public on Mar 22, 2016 |
| Title |
3D7-Input-schizont |
| Sample type |
SRA |
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| Source name |
P. falciparum in vitro culture
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| Organism |
Plasmodium falciparum |
| Characteristics |
strain: 3D7
tissue: whole organism
Stage: Schizont
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| 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.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was purified using Qiagen MinElute columns.
2ng of ChIP or Input material was used to prepare indexed Illumina sequencing libraries using the NEBNext Ultra DNA library prep kit (New England Biolabs). Adapter ligated ChIP DNA libraries were amplified for 15 cycles.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
H3K9ac_Sz_chip_peaks.xls
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| 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
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| Submission date |
Mar 11, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Michaela Petter |
| E-mail(s) |
mpetter@unimelb.edu.au
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| Organization name |
University of Melbourne
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| Department |
Peter Doherty Institute
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| Street address |
792 Elizabeth Street
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| City |
Melbourne |
| State/province |
VIC |
| ZIP/Postal code |
3000 |
| Country |
Australia |
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| 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 |
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| Relations |
| BioSample |
SAMN04571849 |
| SRA |
SRX1651628 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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