|
| Status |
Public on May 05, 2019 |
| Title |
AP2-FG ChIP-seq experiment-1 IP |
| Sample type |
SRA |
| |
|
| Source name |
AP2-FG ChIP-seq experiment-1 IP
|
| Organism |
Plasmodium berghei ANKA |
| Characteristics |
Stage: gametocyte
strain: ANKA
genotype: GFP-fused AP2-FG expressing
antibody: anti-GFP polyclonal antibodies (Abcam)
|
| Treatment protocol |
Six mice were infected with AP2-FG::GFP parasites and treated with sulfadiazine in drinking water (10 mg/ml) for depletion of asexual blood stages.
|
| Growth protocol |
Balb/c mice were infected with P. berghei expressing GFP-fused AP2-FG.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
The infected whole blood was fixed immediately with formalin (1% in final concentration), and erythrocytes were depleted by lysis in 0.85% NH4Cl with changing the solution several times. ChIP was performed according to the protocol in “Standard protocols on Next Generation Sequencing” (edited by Ai Nikaido, Yodosha Co., Ltd., 2014). Briefly, chromatin was sheared by sonication using Bioruptor. Chromatin was IPed with anti-GFP polyclonal antibodies (Abcam) conjugated to Dynabeads Protein A (Life Technologies, Gaithersburg, MD). Obtained DNA fragments were sequenced by the illumina NextSeq sequencer.
Single read - illumina NextSeq 500
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
AP2-FG_ChIP-seq_peaks_exp1.txt
|
| Data processing |
Reads were mapped on the P. berghei genome with allowing one mismatch within 60 bp sequence using Bowtie 2.0. Bedgraph files were ceated from the mapping data (IP).
The mapping data were analyzed with the MACS2 peak-calling algorithm using approximately5.45 × 106 in the experiment-1 and 9.74 × 106 in the experiment-2, respectively.). Numbers of INPUT reads used for normalization were 138 × 107 in the experiment-1 and 1.62 × 107 in the experiment-2, respectively. Conditions for peak calling included an FDR < 0.01 in both experiments.
Genome_build: PlasmoDB, version 9.1
Supplementary_files_format_and_content: Mapping data, bedgraph; Peak-calling, text.
|
| |
|
| Submission date |
May 07, 2018 |
| Last update date |
Oct 26, 2023 |
| Contact name |
masao yuda |
| E-mail(s) |
[email protected]
|
| Organization name |
mie university
|
| Street address |
edobashi 2-174
|
| City |
tsu |
| State/province |
mie |
| ZIP/Postal code |
514-0001 |
| Country |
Japan |
| |
|
| Platform ID |
GPL19670 |
| Series (2) |
| GSE114094 |
Sex-specific gene regulation in malaria parasites by an AP2 Family Transcription Factor [ChIP-Seq] |
| GSE114096 |
Sex-specific gene regulation in malaria parasites by an AP2 Family Transcription Factor |
|
| Relations |
| BioSample |
SAMN09080813 |
| SRA |
SRX4047198 |
