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| Status |
Public on Feb 25, 2024 |
| Title |
HDP1_DIP |
| Sample type |
SRA |
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| Source name |
ANKA
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| Organism |
Plasmodium berghei ANKA |
| Characteristics |
strain: ANKA
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Recombinant homeodomain fused with GST was incubated with P. berghei ANKA genomic DNA fragments in binding/washing buffer (10 μM ZnSO4, 2 mM MgCl2, 2 mM Tris-HCl at pH 7.4, 100 mM KCl, and 10% glycerol) for 30 min. The protein/DNA solution was further mixed with glutathione-sepharose resin and incubated for 30 min. After incubation, the resin was washed three times with binding/washing buffer, and bound protein-DNA complexes were eluted with 10 mM glutathione solution.
Libraries were constructed using KAPA Hyperprep kit (KAPA Biosystems),
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
DNBSEQ-G400 |
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| Data processing |
Reads were mapped on the P. berghei genome using Bowtie 2.0 with default settings. The reads mapped onto multiple sites were removed using grep command. The SAM files were sorted using samtools to produce BAM files. The mapping data were analyzed with the MACS2 peak-calling algorithm.
Assembly: PlasmoDB, version 3
Supplementary files format and content: Peak-calling, text.
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| Submission date |
Feb 20, 2024 |
| Last update date |
Feb 25, 2024 |
| Contact name |
masao yuda |
| E-mail(s) |
m-yuda@doc.medic.mie-u.ac.jp
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| Organization name |
mie university
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| Street address |
edobashi 2-174
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| City |
tsu |
| State/province |
mie |
| ZIP/Postal code |
514-0001 |
| Country |
Japan |
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| Platform ID |
GPL33514 |
| Series (2) |
| GSE235412 |
Chromatin remodeling events associated with gARID are essential for gametocyte development in Plasmodium |
| GSE256093 |
Homeodomain-like domain of Plasmodium berghei HDP1 binds to TGCACA motif. |
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| Relations |
| BioSample |
SAMN39993355 |
| SRA |
SRX23664969 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8085798_HDP1_DIP-seq_peaks_1.xls.gz |
121.4 Kb |
(ftp)(http) |
XLS |
SRA Run Selector |
| Raw data are available in SRA |
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