|
| Status |
Public on Feb 01, 2021 |
| Title |
AP2-G ChIP-seq experiment-1 INPUT |
| Sample type |
SRA |
| |
|
| Source name |
Gametocyte
|
| Organism |
Plasmodium berghei ANKA |
| Characteristics |
tissue: whole body
developmental stage: gametocyte
genotype: GFP-fused AP2-G expressing
chip antibody: None
|
| Growth protocol |
Balb/c mice were synchronously infected with P. berghei expressing GFP-fused AP2-G, and blood was harvested at 18 hpi.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Blood was filtered with Plasmodipur to remove lymphocytes and fixed with 1% formaldehyde for 60 min at 30C with shaking. After erythrocyte lysis in 0.85% NH4Cl, residual cells were subjected to ChIP-seq. Cells were sonicated with Bioruptor in the following condition: total of 20 times at 30 s in middle power in the cell lysis solution containing 1% sodium dodecyl sulfate. The supernatant was subjected to immunoprecipitation with anti-GFP antibodies using Dynabeads protein A.
Libraries were constructed using KAPA Hyperprep kit (KAPA Biosystems), and sequencing was performed with Illumina NEXTseq sequence (Single read - Illumina NextSeq 500).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Reads were mapped on the P. berghei genome with allowing one mismatch within 32 bp sequence using Bowtie 2.0. Bedgraph files were created from the mapping data (IP).
The mapping data were analyzed with the MACS2 peak-calling algorithm using approximately 2.75 × 10e6 in the experiment-1 and 3.39 × 10e6 in the experiment-2. Numbers of INPUT reads used for normalization were 1.35× 10e7 in the experiment-1 and 1.19 × 10e7 in the experiment-2. Conditions for peak calling included an FDR < 0.01 in both experiments.
Genome_build: P. berghei (PlasmoDB, version 3)
Supplementary_files_format_and_content: Mapping data, bedgraph; Peak-calling, text.
|
| |
|
| Submission date |
Feb 07, 2020 |
| Last update date |
Feb 01, 2021 |
| Contact name |
Tsubasa Nishi |
| E-mail(s) |
[email protected]
|
| Organization name |
Mie university
|
| Street address |
Edobashi
|
| City |
Tsu |
| State/province |
Mie |
| ZIP/Postal code |
5140001 |
| Country |
Japan |
| |
|
| Platform ID |
GPL19670 |
| Series (2) |
| GSE144970 |
Mechanisms of Triggering Malaria Gametocytogenesis by AP2-G [ChIP-seq] |
| GSE144971 |
Mechanisms of Triggering Malaria Gametocytogenesis by AP2-G |
|
| Relations |
| BioSample |
SAMN14068494 |
| SRA |
SRX7694932 |
