|
| Status |
Public on Dec 30, 2020 |
| Title |
RNA_Ring rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Asexual stages
|
| Organism |
Plasmodium falciparum |
| Characteristics |
developmental stage: Ring 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 |
SAMN08288509 |
| SRA |
SRX3528867 |
