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EPD viewer for P. falciparum (Apr 2016 ASM276v2/pfa2), version 001

The EPD viewer for P. falciparum is made of the tracks given in the table below. The genome sequence track is provided by the EPD team (sequence was downloaded here). Note that when strand is n/a, it means that signal applies to both strands.

UCSC track name Track description Track resolution [bp] Strand Original dataset Raw format Tissue Stage/Time point Condition MGA series name PMID
1 All MNase centered MNase-seq tagsa 10 n/a GSE66185 SRA n/a all time points merged n/akensche16 26578577
track subset: MNase tags at various time points
2 MNase at 5h centered MNase-seq tags 10 n/a GSM1616484 SRA n/a IDC-5 h n/akensche16 26578577
3 MNase at 10h centered MNase-seq tags 10 n/a GSM1616485 SRA n/a IDC-10 h n/akensche16 26578577
4 MNase at 15h centered MNase-seq tags 10 n/a GSM1616486 SRA n/a IDC-15 h n/akensche16 26578577
5 MNase at 20h centered MNase-seq tags 10 n/a GSM1616487 SRA n/a IDC-20 h n/akensche16 26578577
6 MNase at 25h centered MNase-seq tags 10 n/a GSM1616488 SRA n/a IDC-25 h n/akensche16 26578577
7 MNase at 30h centered MNase-seq tags 10 n/a GSM1616489 SRA n/a IDC-30 h n/akensche16 26578577
8 MNase at 35h centered MNase-seq tags 10 n/a GSM1616490 SRA n/a IDC-35 h n/akensche16 26578577
9 MNase at 40h centered MNase-seq tags 10 n/a GSM1616491, GSM1616492 SRA n/a IDC-40 h n/akensche16 26578577
10 All CAGE (+) 5′ end of CAGE reads 1 + GSE68982 BEDGRAPH n/a all time points merged n/aadjalley16 26947071
11 All CAGE (-) 5′ end of CAGE reads 1 GSE68982 BEDGRAPH n/a all time points merged n/aadjalley16 26947071
track subset: CAGE tags at various time points
12 CAGE at 2h (+) 5′ end of CAGE reads 1 + GSM1689659, GSM1689665 BEDGRAPH n/a IDC-2 h n/aadjalley16 26947071
13 CAGE at 10h (+) 5′ end of CAGE reads 1 + GSM1689660, GSM1689666 BEDGRAPH n/a IDC-10 h n/aadjalley16 26947071
14 CAGE at 18h (+) 5′ end of CAGE reads 1 + GSM1689661, GSM1689667 BEDGRAPH n/a IDC-18 h n/aadjalley16 26947071
15 CAGE at 26h (+) 5′ end of CAGE reads 1 + GSM1689662, GSM1689668 BEDGRAPH n/a IDC-26 h n/aadjalley16 26947071
16 CAGE at 34h (+) 5′ end of CAGE reads 1 + GSM1689663, GSM1689669 BEDGRAPH n/a IDC-34 h n/aadjalley16 26947071
17 CAGE at 42h (+) 5′ end of CAGE reads 1 + GSM1689664, GSM1689670 BEDGRAPH n/a IDC-42 h n/aadjalley16 26947071
18 CAGE at 2h (-) 5′ end of CAGE reads 1 GSM1689659, GSM1689665 BEDGRAPH n/a IDC-2 h n/aadjalley16 26947071
19 CAGE at 10h (-) 5′ end of CAGE reads 1 GSM1689660, GSM1689666 BEDGRAPH n/a IDC-10 h n/aadjalley16 26947071
20 CAGE at 18h (-) 5′ end of CAGE reads 1 GSM1689661, GSM1689667 BEDGRAPH n/a IDC-18 h n/aadjalley16 26947071
21 CAGE at 26h (-) 5′ end of CAGE reads 1 GSM1689662, GSM1689668 BEDGRAPH n/a IDC-26 h n/aadjalley16 26947071
22 CAGE at 34h (-) 5′ end of CAGE reads 1 GSM1689663, GSM1689669 BEDGRAPH n/a IDC-34 h n/aadjalley16 26947071
23 CAGE at 42h (-) 5′ end of CAGE reads 1 GSM1689664, GSM1689670 BEDGRAPH n/a IDC-42 h n/aadjalley16 26947071
24 EPDnew promoters EPDnew promoters v. 001 1b n/ac n/a n/a n/a n/a n/aepd 23193273
25 GC content (%) GC content in a 20-bp window 5d n/a n/a n/a n/a n/a n/an/an/a
26 RefSeq genes RefSeq gene annotation 1 n/a ftp.ncbi.n... GFF n/a n/a n/an/a 22121212
IDC, intraerythrocytic developmental cycle
athe midpoint between paired-end fragments was calculated
bthe thick part represents the TSS plus the 10 bp downstream while the thin part represents the 49 bp upstream of the TSS
cpromoters on the + and − strands are combined in a single track, with promoter orientation defined by the position of the thick part relative to the thin part
dGC content is computed every 5 bp with a 20-bp window

These tracks are available at UCSC as a public hub named "EPD Viewer Hub".

Last update October 2019