ExperimentSetReplicate

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., bioRxiv 2022

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

Quality Metrics

Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Report
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%