|
Status |
Public on Aug 01, 2022 |
Title |
Sample 1 H3K4me3 CUT&RUN |
Sample type |
SRA |
|
|
Source name |
early Schizonts
|
Organism |
Plasmodium falciparum |
Characteristics |
tissue: early Schizonts strain: NF54 pfpeg4-tdTomato chip antibody: H3K4me3 Rabbit Polyclonal antibody ChIP-grade, Diagenode C15410003-50 treatment: none
|
Treatment protocol |
none
|
Growth protocol |
synchronous early schizonts
|
Extracted molecule |
genomic DNA |
Extraction protocol |
1e7 parasites were used per sample for cut & run Libraries were prepared according to Illumina's instructions accompanying the KAPA library preparation kit (KK8230) and sequenced at PE75 on a NextSeq500 machine
|
|
|
Library strategy |
OTHER |
Library source |
genomic |
Library selection |
other |
Instrument model |
Illumina NextSeq 500 |
|
|
Data processing |
Reads in sequenced libraries were checked for quality with FASTQC v0.11.9, adapter and quality-trimmed with trimmomatic v0.39 Properly paired reads were aligned against P.falciparum 3D7 genome v51 with bwa v.0.7.17 and sorted by name using samtools v1.13 Differential genome-wide enrichment between relative to matched isotype controls was calculated using macs2 v2.2.7.1 to generate poisson-based FDR and fold-enrichment tracks and significant peaks Peak annotation and visualization were carried out in R using GenomicRanges v1.44.0, Gviz v1.36.1, and ChIPpeakAnno v3.26.2 packages from Bioconductor using P.falciparum 3D7 genome annotation v51 from PlasmoDB Assembly: Plasmodium falciparum 3D7 v51 from PlasmoDB Supplementary files format and content: bedgraph Library strategy: Cut&Run
|
|
|
Submission date |
Jul 29, 2022 |
Last update date |
Oct 12, 2022 |
Contact name |
Bjorn FC Kafsack |
Organization name |
Weill Cornell Medicine
|
Department |
Microbiology & Immunology
|
Street address |
1300 York Avenue
|
City |
New York |
State/province |
NY |
ZIP/Postal code |
10065 |
Country |
USA |
|
|
Platform ID |
GPL21298 |
Series (1) |
GSE210062 |
Global Profiling of Histone Modifications in Plasmodium falciparum using CUT&RUN. |
|
Relations |
BioSample |
SAMN30050936 |
SRA |
SRX16731135 |