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Status |
Public on Jun 30, 2023 |
Title |
gARID_gsnf2(-)_IP(anti-GFP)_2 |
Sample type |
SRA |
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|
Source name |
gARID::GFP_gsnf2(-)
|
Organism |
Plasmodium berghei ANKA |
Characteristics |
Stage: Gametocyte strain: ANKA genotype: GFP-fused gARID expressing, gsnf2 knockout chip antibody: anti-GFP
|
Treatment protocol |
Infected mice were treated with sulfadiazine for 2 days.
|
Growth protocol |
Balb/c mice were infected with transgenic parasites.
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Whole blood was withdrawn from infected mice, diluted in medium, and filtered with Plasmodipur to remove lymphocytes. The samples were then fixed with 1% formaldehyde for 60 min at 30 °C with shaking. After erythrocyte lysis in 0.85% NH4Cl, residual cells were lysed in SDS lysis buffer. The lysates were sonicated with Bioruptor in the following condition: total of 20 times at 30 s in middle power. After centrifugation of the sonicated lysates, the supernatants were subjected to immunoprecipitation with anti-GFP antibodies conjugated on 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),
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|
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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 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 |
Jun 21, 2023 |
Last update date |
Jun 30, 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) |
GSE235409 |
Chromatin remodeling events associated with gARID are essential for gametocyte development in Plasmodium [ChIP-seq] |
GSE235412 |
Chromatin remodeling events associated with gARID are essential for gametocyte development in Plasmodium |
|
Relations |
BioSample |
SAMN35816669 |
SRA |
SRX20734507 |