Kensche 2016, MNase sequencing at eight time points during the IDC of Plasmodium falciparum.


Paired-end sequencing of MNase-treated chromatin from the malaria parasite P. falciparum at 8 stages of its intra-erythrocytic developmental cycle (IDC) at 5 h intervals.



From P. falciparum (Apr 2016 ASM276v2/pfa2).

DNase FAIRE data:

Filename Description Feature GEO-ID
1 GSE66185_all.sga IDC|MNase|all samples MNase -
2 GSE66185_147bp_all.sga IDC|MNase|all samples 147bp fragments MNase -
3 GSE66185_oriented_all.sga IDC|MNase|all samples oriented MNase -
4 GSM1616484.sga IDC|MNase|5h MNase GSM1616484
5 GSM1616485.sga IDC|MNase|10h MNase GSM1616485
6 GSM1616486.sga IDC|MNase|15h MNase GSM1616486
7 GSM1616487.sga IDC|MNase|20h MNase GSM1616487
8 GSM1616488.sga IDC|MNase|25h MNase GSM1616488
9 GSM1616489.sga IDC|MNase|30h MNase GSM1616489
10 GSM1616490.sga IDC|MNase|35h MNase GSM1616490
11 GSM1616491.sga IDC|MNase|40h|rep1 MNase GSM1616491
12 GSM1616492.sga IDC|MNase|40h|rep2 MNase GSM1616492

Technical Notes

FASTQ files were extracted from SRA files using fastq-dump (SRA toolkit v2.5.0) and mapped to the genome using Bowtie v1.1.1. SAM files were then converted into BAM using samtools v0.1.14 and to bed using bamToBed v2.27.0 (bedtools). SGA conversion was carried out using in-house software.


Last update: 4 Dec 2018