ExperimentSetReplicate

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ExperimentSet4DNESA85FV7T
released
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H3K4me3 PLAC-seq on C57BL/6NCrl embryonic day 12.5 mouse liver

   April 24th, 2022 at 12:21am
Source Publication
Integrative analysis of the 3D genome and epigenome in mouse embryonic tissues.
Yu M, Zemke NR, et al., Nature structural & molecular biology 2024

Experiment Set Properties  

Set Type 
Replicate
Organism 
M. musculus
Sample Type 
tissue
Sample 
liver
Experiment Type(s) 
PLAC-seq
Modification Type 
None
Treatment Type 
None
Assay Details 
Target: H3K4me3 (mouse)

7 Processed Files

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Experiment
File
File Type
File Size
Notes
From Multiple Experiments
4DNESA85FV7T
Multiple Experiments
File
4DNFIGDDHN33
contact list-combined (pairs)
5.3 GB
-
File
4DNFIVNTGU2E
contact matrix (hic)
2.96 GB
-
File
4DNFI2UGGTDD
contact matrix (mcool)
1.94 GB
Experiment
4DNEXHH58O4I
Bio Rep 1, Tec Rep 1
PLAC-seq against H3K4me3 (mouse) on liver
File
4DNFIO1BUNMY
alignments (bam)
47.69 GB
-
File
4DNFIWH5J3VR
contact list-replicate (pairs)
3.35 GB
-
Experiment
4DNEXPTZ1XYH
Bio Rep 2, Tec Rep 1
PLAC-seq against H3K4me3 (mouse) on liver
File
4DNFIAGB8RZL
alignments (bam)
44.06 GB
-
File
4DNFI9II57DG
contact list-replicate (pairs)
2.29 GB
-

Quality Metrics

Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Details
From Multiple Experiments
4DNESA85FV7T
Multiple Experiments
File
Contact List-combined (pairs)
4DNFIGDDHN33
286.31m
52.071%
17.179%
30.749%
Experiment
4DNEXHH58O4I
Bio Rep 1, Tec Rep 1
PLAC-seq against H3K4me3 (mouse) on liver
File
Contact List-replicate (pairs)
4DNFIWH5J3VR
169.62m
51.416%
16.658%
31.926%
Experiment
4DNEXPTZ1XYH
Bio Rep 2, Tec Rep 1
PLAC-seq against H3K4me3 (mouse) on liver
File
Contact List-replicate (pairs)
4DNFI9II57DG
116.69m
53.023%
17.937%
29.04%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNESA85FV7T
Multiple Experiments
File
Contact Matrix (mcool)
4DNFI2UGGTDD
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
4DNEXHH58O4I
Bio Rep 1, Tec Rep 1
PLAC-seq against H3K4me3 (mouse) on liver
File
Alignments (bam)
4DNFIO1BUNMY
290.03m
17.665%
16.272%
2.587%
4.992%
0.121%
Experiment
4DNEXPTZ1XYH
Bio Rep 2, Tec Rep 1
PLAC-seq against H3K4me3 (mouse) on liver
File
Alignments (bam)
4DNFIAGB8RZL
209.97m
21.698%
10.868%
3.611%
8.246%
0.09%