|
| Status |
Public on Oct 06, 2021 |
| Title |
Trophozoite_InputDNA |
| Sample type |
SRA |
| |
|
| Source name |
Asexual stages
|
| Organism |
Plasmodium falciparum |
| Characteristics |
developmental stage: Trophozoite stage
strain: T996
chip antibody: None
|
| 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 |
genomic DNA |
| Extraction protocol |
Libraries for ChIP-Seq were prepared using NEBNext Ultra DNA library prep kit from Illumina
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina MiSeq |
| |
|
| Data processing |
Paired-end reads from ChIP-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).
Alignments with a MAPQ of 10 and properly paired were extracted using Samtools (Version 1.3).
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
|
| |
|
| Submission date |
Oct 06, 2021 |
| Last update date |
Oct 07, 2021 |
| Contact name |
Mark Stephen Featherstone |
| E-mail(s) |
msfeatherstone@gmail.com
|
| Phone |
5102982825
|
| Organization name |
Nanyang Technological University
|
| Department |
School of Biological Sciences
|
| Street address |
60 Nanyang Drive
|
| City |
Singapore |
| State/province |
Singapore |
| ZIP/Postal code |
637551 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL19269 |
| Series (1) |
| GSE108716 |
Genome-wide mapping of RNAPII and its phosphoisoforms in Plasmodium falciparum |
|
| Relations |
| BioSample |
SAMN22082213 |
| SRA |
SRX12498516 |
