|
| Status |
Public on Aug 01, 2022 |
| Title |
Sample 2 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 |
SAMN30050933 |
| SRA |
SRX16731138 |
