|
Status |
Public on Oct 28, 2010 |
Title |
P.falciparum_3D7_ChIPseq_input_30hpi |
Sample type |
SRA |
|
|
Source name |
Asexual stages
|
Organism |
Plasmodium falciparum 3D7 |
Characteristics |
develpmental stage: 30hpi
|
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 |
MNase-Seq |
Library source |
genomic |
Library selection |
MNase |
Instrument model |
Illumina Genome Analyzer II |
|
|
Description |
MNase-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 |
SRX026773 |
BioSample |
SAMN00113315 |