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| Status |
Public on Feb 02, 2022 |
| Title |
3D7_AP2-EXP2-GFP_S_input |
| Sample type |
SRA |
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| Source name |
schizont (40–45 hpi)
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| Organism |
Plasmodium falciparum |
| Characteristics |
tissue: whole body
developmental stage: schizont (40-45 hpi)
strain: Pf 3D7
genotype: AP2-EXP2-GFP
host: Homo sapiens
chip antibody: None
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| Treatment protocol |
Ring stage cultures were regularly synchronized by treatments of 5% sorbitol.
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| Growth protocol |
Parasites were cultured in fresh O-type human erythrocytes in complete RPMI 1640 medium (Gibco) with 0.5% Albumax I (Invitrogen) and a gas phase maintained under 5% CO2, 5% O2 and 90% N2 at 37°C.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Synchronized parasites were harvested at the schizont stage (40-45 hpi) and crosslinked immediately with 1% paraformaldehyde (Sigma) by rotating for 10 minutes at 37°C, which was then quenched with 0.125 M glycine for 5 minutes on ice. Parasite nuclei released from infected red blood cells were sheared for 20-30 minutes using an M220 sonicator (Covaris) at 5% duty cycle, 200 cycles per burst, and 75 W of peak incident power to generate 100-500 bp fragments in length. 20 µL of the sheared chromatin was reserved as the input control. Chromatin was subsequently immunoprecipitated overnight at 4°C using 0.5 µg of antibodies against GFP (Abcam, ab290) and protein A/G magnetic beads (ThermoFisher Scientific, 26162). After extensive washes, the immunoprecipitated materials were eluted with elution buffer. Then crosslinking was reversed by overnight incubation at 45°C, followed by treatments of RNase A at 37°C for 30 minutes and Proteinase K at 45°C for two hours. The ChIPped DNA was finally purified according to the MinElute PCR purification kit (Qiagen, 28006) instructions.
1.5 ng of ChIP-DNA was subjected to end-repair (Epicentre, ER81050), 3' adenylation (NEB, M0212L), and adapter ligation (NEB, M2200L). Then after purification with Agencourt AMPure XP beads (Beckman Coulter), libraries were amplified using the KAPA HiFi PCR Kit (KAPA Biosystems, KB2500) under the following conditions: 1 minute of initial denaturation at 98°C, 12 cycles of 10 seconds at 98°C and 1 minute at 65°C, and 5 minutes of final extension at 65°C.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
HiSeq X Ten |
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| Description |
3D7_AP2-EXP2-GFP_S_input
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| Data processing |
To remove residual adapters and low-quality bases, sliding window trimming was performed on reads with Trimmomatic v0.39 using a window size of 4 and average quality of the window above 15. A minimum read length of 50 bp and average read quality above 20 were required after read clipping.
Trimmed ChIP-seq reads were mapped to the P. falciparum 3D7 reference genome (release 47) using Bowtie2 v2.4.2 and default parameters.
Peaks were identified using the callpeak function of MACS2 v2.2.7.1 and a q-value cutoff of 0.05. The option --call-summits was applied to the detection of transcription factor binding peaks. Normalized signal tracks of log2-transformed ChIP/input fold enrichment were generated with MACS2 bdgcmp function.
Genome_build: Pf 3D7 v47
Supplementary_files_format_and_content: bigWig files of log2-transformed ChIP/input fold enrichment
Supplementary_files_format_and_content: BED files of peak summits
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| Submission date |
Jul 20, 2021 |
| Last update date |
Feb 04, 2022 |
| Contact name |
Mei Jiang |
| E-mail(s) |
gingerplum@hotmail.com
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| Phone |
862165985138
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| Organization name |
Tongji University
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| Street address |
1239 Siping Road
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| City |
Shanghai |
| State/province |
Shanghai |
| ZIP/Postal code |
200092 |
| Country |
China |
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| Platform ID |
GPL26835 |
| Series (2) |
| GSE180437 |
Roles of PfAP2-EXP2 in Plasmodium falciparum blood-stage development [ChIP-seq] |
| GSE180438 |
Roles of PfAP2-EXP2 in Plasmodium falciparum blood-stage development |
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| Relations |
| BioSample |
SAMN20322111 |
| SRA |
SRX11503860 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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