|
| Status |
Public on Feb 18, 2020 |
| Title |
Input_ChIP-Seq_AP2-G_GFP_E1_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
In vitro cultured blood stage cells
|
| Organism |
Plasmodium falciparum |
| Characteristics |
genotype: AP2-G-GFP
chip antibody: None
|
| Growth protocol |
Blood stage P. falciparum parasites were cultured in human O+ red blood cells in RPMI-1640 medium supplemented with Albumax II (10% v/v), hypoxanthine (200 μM) and gentamycin (50 μg/ml) in 3% CO2 and 5% O2 at 37 °C.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP was performed as previously described (Zanghi et al, 2018 Cell. Rep.) with parasites synchronised at 36 hpi. Sonicated chromatin (500 ng DNA content) was immunoprecipitated overnight with 0.5 μg of anti-HP1 polyclonal rabbit antibodies. and incubated after with 25 μl of Dynabeads Protein G (Invitrogen) for two hours. Subsequent washing, cross-link reversion and DNA extraction were carried out as described before.
Sequencing libraries were produced with the immunoprecipitated DNA using the MicroPlex Library Preparation Kit v2 (Diagenode) with the KAPA HiFi polymerase (Kapa Biosystems) for the PCR amplification. For each ChIP sample, a control DNA corresponding to the ChIP input was processed in parallel.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Input_ChIP-Seq_AP2-G_GFP_E1_rep2
E1_HP1_2_FE.bigWig
|
| Data processing |
Demultiplexing with bcl2fastq (Illumina) software v2.19.1.403
ChIP-Seq reads aligned to the genome using BWA v0.7.10-r789 with default parameters
Data sorted, indexed and PCR duplicates filteres using samtools v1.3
Peak calling (callpeak option) and calculation of fold enrichment over input (bdgcmp option) performed with MACS2 (v2.1.1.20160309) software using -BAMPE and --SPMR options.
Genome_build: PlasmoDB-29_Pfalciparum3D7
Supplementary_files_format_and_content: BigWig files obtained using bedGraphToBigWig software v4
|
| |
|
| Submission date |
Feb 17, 2020 |
| Last update date |
Mar 10, 2020 |
| Contact name |
Carlos Cordon-Obras |
| E-mail(s) |
obsidian1983@gmail.com
|
| Organization name |
Instituto Parasitologia Lopez Neyra
|
| Street address |
Av del Conocimiento
|
| City |
Granada |
| ZIP/Postal code |
18016 |
| Country |
Spain |
| |
|
| Platform ID |
GPL21298 |
| Series (1) |
| GSE145378 |
An exon DNA element modulates heterochromatin spreading in the master regulator for sexual commitment in malaria parasites |
|
| Relations |
| BioSample |
SAMN14120227 |
| SRA |
SRX7734638 |
