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Sample GSM588514 Query DataSets for GSM588514
Status Public on Oct 28, 2010
Title P.falciparum_3D7_ChIPseq_H2A_40hpi
Sample type SRA
 
Source name Asexual stages
Organism Plasmodium falciparum 3D7
Characteristics strain: 3D7/Ty1-H2A
develpmental stage: 40hpi
antibody: antiTy
antibody manufacturer: a mouse monoclonal antibody named BB2, which we received from Prof Keith Gull. Ref: Bastin, P., Bagherzadeh, A., Matthews, K. R. and Gull, K. (1996b). A novel epitope tag system to study protein targeting and organelle biogenesis in Trypanosoma brucei. Mol. Biochem. Parasitol. 77, 235-239.
Growth protocol Parasites were cultured in standard RPMI medium supplemented with 10% human serum and 0.2% NaHCO3 in 20ml per 250ml tissue culture flasks and candle jars. The culture was synchronised with multiple rounds of sorbitol treatments and Percoll gradient centrifugation.
Extracted molecule genomic DNA
Extraction protocol Native chromatin was diggested with MNase and immunoprecipitated using the indicated antisera. Immunoprecipitated DNA fragments were purified and sequenced using a T7- polymerase based library preparation protocol.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer II
 
Description native ChIP-seq
Data processing Reads (76 bp) were aligned to the P.falciparum (3D7) genome (PlasmoDB v6.1) using BWA. Datasets for different stages were equalized for the total number of uniquely mapped tags (5,5M for ChIP-seq and 11M for MNase-seq) by random removal of sequenced tags. GFF files were generated from these BED files.
 
Submission date Aug 30, 2010
Last update date May 15, 2019
Contact name H.G. Stunnenberg
E-mail(s) h.stunnenberg@ncmls.ru.nl
Phone +31-24-3610520
Organization name Radboud University
Department Department of Molecular Biology (274)
Street address Geert Grooteplein 28
City Nijmegen
ZIP/Postal code 6525 GA
Country USA
 
Platform ID GPL10866
Series (2)
GSE23787 H2A.Z Demarcates Intergenic Regions of the Plasmodium falciparum Epigenome That Are Dynamically Marked by H3K9ac and H3K4me3
GSE23867 Epigenetic profile of the Plasmodium falciparum intraerythrocytic cycle
Relations
SRA SRX026762
BioSample SAMN00113304

Supplementary file Size Download File type/resource
GSM588514_P.falciparum_3D7_ChIPseq_H2A_40hpi.bed.gz 22.8 Mb (ftp)(http) BED
GSM588514_P.falciparum_3D7_ChIPseq_H2A_40hpi.gff.gz 12.7 Mb (ftp)(http) GFF
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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