|
| Status |
Public on Oct 01, 2015 |
| Title |
AP2-G2 ChIP-seq experiment-1 IP |
| Sample type |
SRA |
| |
|
| Source name |
AP2-G2 ChIP
|
| Organism |
Plasmodium berghei ANKA |
| Characteristics |
strain: ANKA
Stage: gametocyte
genotype: GFP-fused AP2-G2 expressing
host mouse strain: Balb/c
chip antibody: Anti-GFP
chip antibody vendor: Abcam
chip antibody cat. #: ab290
chip antibody lot #: GR19413-1
|
| Treatment protocol |
Sulfadiazine was added to their drinking water (10 mg/L) in order to deplete asexual blood-stage parasites. When the exflagellation of the male gametes reached approximately 300 per 1 μL of blood, the blood was harvested and cultured in an ookinete culture medium for 16 h, and then fixed with 1% paraformaldehyde.
|
| Growth protocol |
Balb/c mice were pre-treated with phenylhydrazine and then infected with P. berghei expressing GFP-fused AP2-G2.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Erythrocytes in the fixed culture were removed by lysis in 0.84% NH4Cl, and the remaining ookinetes were subjected to ChIP. ChIP was performed using the ChIP Assay Kit (Millipore, USA) according to the manufacturer’s protocol. Briefly, samples in the lysis buffer were sonicated with a Bioruptor (Tosho Denki, Yokohama, Japan) until chromatin DNA was fragmented to 150 bp for sequencing with a SOLID 5500 system (Life Technologies). Immunoprecipitation (IP) was performed with anti-GFP antibodies, and the harvested DNA fragments were subjected to sequencing. Input DNAs were obtained from the chromatin without IP. Anti-GFP antibodies used for ChIP were purchased from Abcam (Cat. No. ab290, Lot No.GR19413-1).
Single read - SOLiD 5500 (ABI)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
AB 5500 Genetic Analyzer |
| |
|
| Data processing |
Sequence data were mapped onto the P. berghei genome sequence (PlasmoDB, version 9.1) with a complete match within 60 bp using in-house scripts. Bedgraph files were ceated from the mapping data (IP).
The mapping data were analyzed with the MACS2 peak-calling algorithm using approximately 0.5 × 107 reads (IP). Numbers of INPUT reads used for normalization were 2.3 × 107 in the experiment-1 and 1.5 × 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 |
Feb 23, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
masao yuda |
| E-mail(s) |
m-yuda@doc.medic.mie-u.ac.jp
|
| Organization name |
mie university
|
| Street address |
edobashi 2-174
|
| City |
tsu |
| State/province |
mie |
| ZIP/Postal code |
514-0001 |
| Country |
Japan |
| |
|
| Platform ID |
GPL19817 |
| Series (2) |
| GSE66189 |
Global Transcriptional Repression: Initial and Essential Step for Plasmodium Sexual Development [ChIP-seq] |
| GSE66190 |
Global Transcriptional Repression: Initial and Essential Step for Plasmodium Sexual Development |
|
| Relations |
| BioSample |
SAMN03366087 |
| SRA |
SRX885867 |
