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| Status |
Public on Apr 11, 2018 |
| Title |
Chromatin accessibility based characterization of gene regulatory network of P. falciparum blood stage development |
| Organism |
Plasmodium falciparum |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
We present ATAC-seq combined with direction RNA seq data for eight time points across the intraerythorcytic development cycle of Plasmodium falciparum 3D7. ATAC peaks were called by MACS2 using ATAC-seq libraries generated with genomic DNA as a control. The majority of identified ATAC peaks were located in intergenic regions and captured most (95%) of previously identified binding sites of the transcription factor required for the expression of most invasion-related genes PfAP2-I (Santos et al., 2017). The robustness of the ATAC-seq dataset was confirmed with a second biological replicate both in terms of peak location and relative peak accessibility pattern. Peaks were assigned to the closest gene and the majority of peaks showed a clear positive correlation between chromatin accessibility pattern and relative mRNA abundance (Pearson correlation > 0.6). In addition, they were sufficient to drive the stage-specific expression of a reporter gene, demonstrating their functionality. Motif searches restricted to accessible regions showed enrichment of several predicted Plasmodium motifs while also predicting several novel regulatory elements.
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| Overall design |
ATAC-seq and RNA-seq at 8 time points across the intraerytrocytic development cycle of P. falciparum 3D7 .
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| Contributor(s) |
Bártfai R, Toenhake CG, Fraschka SK |
| Citation(s) |
29649445 |
| Submission date |
Sep 20, 2017 |
| Last update date |
Jul 25, 2021 |
| Contact name |
Christa Toenhake |
| E-mail(s) |
c.toenhake@science.ru.nl
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| Organization name |
Radboud University
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| Department |
Molecular Biology
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| Street address |
Geert Grooteplein 28
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| City |
Nijmegen |
| State/province |
Netherlands |
| ZIP/Postal code |
6525 GA |
| Country |
Netherlands |
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| Platforms (1) |
| GPL21298 |
Illumina NextSeq 500 (Plasmodium falciparum) |
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| Samples (26)
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| GSM2789024 |
Pf-3D7-t20, ATACseq |
| GSM2789025 |
Pf-3D7-t25, ATACseq |
| GSM2789026 |
Pf-3D7-t30, ATACseq |
| GSM2789027 |
Pf-3D7-t35, ATACseq |
| GSM2789028 |
Pf-3D7-t40, ATACseq |
| GSM2789029 |
Pf-3D7-gDNA-a, ATACseq |
| GSM2789030 |
Pf-3D7-gDNA-b, ATACseq |
| GSM2789031 |
Pf-3D7-t05, dirRNAseq |
| GSM2789032 |
Pf-3D7-t10, dirRNAseq |
| GSM2789033 |
Pf-3D7-t15, dirRNAseq |
| GSM2789034 |
Pf-3D7-t20, dirRNAseq |
| GSM2789035 |
Pf-3D7-t25, dirRNAseq |
| GSM2789036 |
Pf-3D7-t30, dirRNAseq |
| GSM2789037 |
Pf-3D7-t35, dirRNAseq |
| GSM2789038 |
Pf-3D7-t40, dirRNAseq |
| GSM2987661 |
Pf-3D7-t05, ATACseq, replicate2 |
| GSM2987662 |
Pf-3D7-t10, ATACseq, replicate2 |
| GSM2987663 |
Pf-3D7-t15, ATACseq, replicate2 |
| GSM2987664 |
Pf-3D7-t20, ATACseq, replicate2 |
| GSM2987665 |
Pf-3D7-t25, ATACseq, replicate2 |
| GSM2987666 |
Pf-3D7-t30, ATACseq, replicate2 |
| GSM2987667 |
Pf-3D7-t35, ATACseq, replicate2 |
| GSM2987668 |
Pf-3D7-t40, ATACseq, replicate2 |
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| Relations |
| BioProject |
PRJNA408158 |
| SRA |
SRP118379 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE104075_Pf-3D7-alltp_8tpATACseq.peaks.bed.gz |
43.6 Kb |
(ftp)(http) |
BED |
| GSE104075_Pf-3D7-alltp_8tpATACseq.summits.bed.gz |
58.9 Kb |
(ftp)(http) |
BED |
| GSE104075_RAW.tar |
1.4 Gb |
(http)(custom) |
TAR (of BED, BEDGRAPH) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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