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Sample GSM7501972 Query DataSets for GSM7501972
Status Public on Jun 30, 2023
Title gARID_gsnf2(-)_IP(anti-GFP)_2
Sample type SRA
 
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Extraction protocol Whole blood was withdrawn from infected mice, diluted in medium, and filtered with Plasmodipur to remove lymphocytes.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),
 
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.
 
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

Supplementary file Size Download File type/resource
GSM7501972_gARID_gsnf2_-_ChIP-seq_peaks_2.txt.gz 117.4 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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