|
| Status |
Public on Nov 09, 2021 |
| Title |
PfBDP1HA::PfBDP7BirATy_anti-Ty_mature S |
| Sample type |
SRA |
| |
|
| Source name |
P. falciparum in vitro culture
|
| Organism |
Plasmodium falciparum |
| Characteristics |
parasite line: PfBDP1HA::PfBDP7BirATy
Stage: mature schizont
|
| Growth protocol |
Plasmodium falciparum parasites were cultured in RPMI-HEPES medium containing 5% O+ red blood cells, 0.2% sodium bicarbonate and 0.25% Albumax (Gibco) and 5% human serum (AB+). Parasitaemia was maintained at 0.5%-10%. Parasites cultures were incubated at 37ºC in 1% O2, 5% CO2 and 94% N2.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cultures were fixed with 1% PFA and nuclei were isolated. Chromatin was fragmented by sonication before immunoprecipitation of Protein/DNA complexes.
Libraries were generated using the Accel2S PLUS DNA Library kit (Swift Biosciences). Library amplification was performed using the KAPA Hifi PCR kit (KK2101) according to published procedures (PMID: 26067602).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Accel2S Ultra DNA library kit
|
| Data processing |
Quality control of samples using FastQC version 0.11.8
Trimming using TrimGalore version 0.6.5 and Cutadapt version 2.8
Mapping with Bowtie2 version 2.3.5.1 against Plasmdium genome version 28
BAM files with Samtools version 1.2
Bigwig files of log2 ratios with Deeptools version 3.3.1
Genome_build: PlasmoDB-28_Pfalciparum3D7_Genome.fasta / PlasmoDB-28_Pfalciparum3D7.gff (available on PlasmoDB)
Supplementary_files_format_and_content: Bigwig files with Log2 ratio ChIP/Input
|
| |
|
| Submission date |
Nov 02, 2021 |
| Last update date |
Nov 09, 2021 |
| Contact name |
Michaela Petter |
| E-mail(s) |
michaela.petter@uk-erlangen.de
|
| Phone |
+4991318522177
|
| Organization name |
Univeritätsklinikum Erlangen
|
| Department |
Mirkobiologisches Institut
|
| Street address |
Wassertrumstr. 3-5
|
| City |
Erlangen |
| ZIP/Postal code |
91054 |
| Country |
Germany |
| |
|
| Platform ID |
GPL26836 |
| Series (1) |
| GSE186984 |
ChIPseq of the P. falciparum bromodomain proteins PfBDP7 and PfBDP1 in early and mature schizonts |
|
| Relations |
| BioSample |
SAMN22837110 |
| SRA |
SRX12895037 |
