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Sample GSM2912445 Query DataSets for GSM2912445
Status Public on Dec 30, 2020
Title RNA_Sch1 rep1
Sample type SRA
 
Source name Asexual stages
Organism Plasmodium falciparum
Characteristics developmental stage: Schizont stage
strain: T996
Treatment protocol P. falciparum was formaldehyde cross-linked and 5x108 schizonts,1x109 trophozoites or 2x109 ring stage parasites were harvested for Chromatin immunoprecipitation.
Growth protocol P. falicparum was culture in RPMI at 2% haematocrit and sorbitol synchronized
Extracted molecule total RNA
Extraction protocol RNA from each stage was isolated by Trizol method. Dnase treated RNA was used for preparing library for RNA Seq.Lysates were clarified from sonicated nuclei and RNAPII-DNA complexes were isolated with RNAPII antibodies.
Library preparation for RNA Seq was performed according to Illumina¹s Stranded mRNA sample preparation protocol, following the manufacturer¹s recommendations. Libraries for ChIP-Seq were prepared using NEBNext Ultra DNA library prep kit from Illumina
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Data processing Paired-end reads from ChIP-Seq and RNA-Seq were run through FastQC (Version 0.11.4) to generate quality reports, followed by quality and length trimming using trim_galore (Version 0.4.1).
Reads from ChIP and input DNA samples were mapped to PlasmoDbv9.0 using Bowtie2 (Version 2.2.6). RNA-Seq reads were mapped to the transcriptome of the same version using STAR-aligner (Version 2.5.1b).
Alignments with a MAPQ of 10 and properly paired were extracted using Samtools (Version 1.3). HTSeq-count (Version 0.6.1p1) and DESeq2 were used for read counting and normalization of RNA-Seq data.
Heatmap and profile plots were generated by deepTools (Version 2.3.4)
Peak calling was done using MACS2 (Version 2.1.1) with p = 0.05. Peak to gene annotation was done with bespoke scripts based on Bedtools (Version 2.25.0) suite
Genome_build: PlasmoDbv9.0
Supplementary_files_format_and_content: counts, bigwig, and peaks
 
Submission date Jan 03, 2018
Last update date Dec 30, 2020
Contact name Mark Stephen Featherstone
E-mail(s) msfeatherstone@gmail.com
Organization name Nanyang Technological University
Department School of Biological Sciences
Lab 03n-39
Street address 60, Nanyang Drive
City Singapore
State/province Singapore
ZIP/Postal code 637551
Country Singapore
 
Platform ID GPL21078
Series (1)
GSE108716 Genome-wide mapping of RNAPII and its phosphoisoforms in Plasmodium falciparum
Relations
BioSample SAMN08288504
SRA SRX3528872

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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