ExperimentSetReplicate

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ExperimentSet4DNESVMWQH93
released
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H3K4me3 PLAC-seq on F123 cells

   September 21st, 2018 at 5:06pm
Source Publication
MAPS: Model-based analysis of long-range chromatin interactions from PLAC-seq and HiChIP experiments.
Juric I, Yu M, et al., PLoS computational biology 2019

Experiment Set Properties  

Set Type 
Replicate
Organism 
M. musculus
Sample Type 
stem cells
Sample 
F123-CASTx129 (Tier 2)
Experiment Type(s) 
PLAC-seq
Modification Type 
None
Treatment Type 
None
Assay Details 
Target: H3K4me3

7 Processed Files

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Experiment
File
File Type
File Size
Notes
From Multiple Experiments
4DNESVMWQH93
Multiple Experiments
File
4DNFI8L5VPXG
contact list-combined (pairs)
6.03 GB
-
File
4DNFIFFKJQNV
contact matrix (hic)
1.97 GB
-
File
4DNFIBMH7HPI
contact matrix (mcool)
1.29 GB
Experiment
4DNEXZSEZ9GH
Bio Rep 1, Tec Rep 1
PLAC-seq against H3K4me3 on F123-CASTx129 (Tier 2)
File
4DNFIR2SSMW1
alignments (bam)
83.2 GB
-
File
4DNFIIHRFVI3
contact list-replicate (pairs)
3.43 GB
-
Experiment
4DNEXN4MCFBV
Bio Rep 2, Tec Rep 1
PLAC-seq against H3K4me3 on F123-CASTx129 (Tier 2)
File
4DNFIADEO6TV
alignments (bam)
74.6 GB
-
File
4DNFIFBZFN96
contact list-replicate (pairs)
3.16 GB
-

Quality Metrics

Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Details
From Multiple Experiments
4DNESVMWQH93
Multiple Experiments
File
Contact List-combined (pairs)
4DNFI8L5VPXG
348.52m
51.021%
38.232%
10.747%
Experiment
4DNEXZSEZ9GH
Bio Rep 1, Tec Rep 1
PLAC-seq against H3K4me3 on F123-CASTx129 (Tier 2)
File
Contact List-replicate (pairs)
4DNFIIHRFVI3
181.71m
51.724%
37.665%
10.61%
Experiment
4DNEXN4MCFBV
Bio Rep 2, Tec Rep 1
PLAC-seq against H3K4me3 on F123-CASTx129 (Tier 2)
File
Contact List-replicate (pairs)
4DNFIFBZFN96
166.81m
50.256%
38.848%
10.896%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNESVMWQH93
Multiple Experiments
File
Contact Matrix (mcool)
4DNFIBMH7HPI
1000; 2000; 5000; 10000; 25000; 50000; 100000; 250000; 500000; 1000000; 2500000; 5000000; 10000000
Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEXZSEZ9GH
Bio Rep 1, Tec Rep 1
PLAC-seq against H3K4me3 on F123-CASTx129 (Tier 2)
File
Alignments (bam)
4DNFIR2SSMW1
588.71m
12.819%
17.752%
32.731%
5.832%
0.063%
Experiment
4DNEXN4MCFBV
Bio Rep 2, Tec Rep 1
PLAC-seq against H3K4me3 on F123-CASTx129 (Tier 2)
File
Alignments (bam)
4DNFIADEO6TV
546.49m
12.902%
18.468%
32.381%
5.725%
0.067%