|
| Status |
Public on Jul 15, 2022 |
| Title |
ChIP-seq on AP2-EXP in the AP2-EXP::GFP Pf3D7 background at 30 hpi replicate 1 immunoprecipitate |
| Sample type |
SRA |
| |
|
| Source name |
3D7
|
| Organism |
Plasmodium falciparum |
| Characteristics |
Stage: trophozoite
cell line: 3D7
chip antibody: Abcam Ab290 anti-GFP
|
| Growth protocol |
Parasites were grown at 37°C, 5% O2, 7% CO2 using RPMI1640 media supplemented with hypoxanthine and .5% Albumax II (Thermo). AP2-EXP::GFP and AP2-EXP::HA were maintained in media supplemented with 2.5nM WR99210
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP was performed as described in PMID: 32198457. Briefly, nuclear material was extracted following cross-linking in 1% formaldehyde. Chromatin was sonicated using an M220 ultrasonicator (Covaris) at 5% duty cycle, 75 W peak incident power, 200 cycles per burst, treatment time 300 seconds. Input chromatin was set aside to use as a control, and the remaining material was immunoprecipitated overnight using anti-HA or anti-GFP antibody. RNA and protein were removed by enzymatic digestion and DNA was isolated using the Qiagen MinElute kit.
ChIP-seq DNA libraries were prepared as described in PMID: 32198457 using the NEBNext II DNA library kit (New England Biolabs) according to the manufacturer’s instructions. Quality was assessed using an Agilent 2100 Bioanalyzer or TapeStation. AMPure XP beads (Beckmann Coulter) were used to size select and purify DNA between NEBNext II library preparation steps.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Reads in each DNA library were trimmed to remove low quality base calls and Illumina adaptor sequences using Trimmomatic 0.32.3.
Reads were mapped to the P. falciparum 3D7 genome (Pf 3D7 v36) using BWA-MEM 0.4.1.
Duplicate reads were removed using samtools 1.1.2.
MACS2 (version 2.1.1.20160309) was used to call peaks with a q value cutoff of 0.01.
Deeptools BamCoverage 3.5.1.0.0 was used to generate bigwig files from mapped .bam files.
Assembly: PlasmoDB-36_Pfalciparum3D7_Genome.fasta
Supplementary files format and content: bigwig for all libraries, narrowpeak calls for immunoprecipitate over input
|
| |
|
| Submission date |
Jul 13, 2022 |
| Last update date |
Jul 16, 2022 |
| Contact name |
Timothy J Russell |
| E-mail(s) |
tjr30@psu.edu
|
| Phone |
17742693971
|
| Organization name |
Pennsylvania State University
|
| Street address |
W122 Millennium Science Complex
|
| City |
STATE COLLEGE |
| State/province |
PA |
| ZIP/Postal code |
16802 |
| Country |
USA |
| |
|
| Platform ID |
GPL21078 |
| Series (1) |
| GSE208155 |
Identification of antimalarial compounds that inhibit Apicomplexan AP2 transcription factor proteins in the human malaria parasite Plasmodium falciparum [ChIP-seq] |
|
| Relations |
| BioSample |
SAMN26879066 |
| SRA |
SRX14572788 |
