ExperimentSetReplicate

ExperimentSet4DNESS2HA1AN
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H3K4me3 PLAC-seq on C57BL/6NTac;6NCrl/Lap embryonic day 14.5 mouse forebrain

   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 
forebrain
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
4DNESS2HA1AN
Multiple Experiments
File
Contact List-combined (pairs)
4DNFIIII16YT
287.39m
48.244%
22.394%
29.361%
Experiment
4DNEXEE5G2C7
Bio Rep 1, Tec Rep 1
PLAC-seq against H3K4me3 (mouse) on forebrain
File
Contact List-replicate (pairs)
4DNFI7ONPRLV
187.5m
47.092%
23.724%
29.184%
Experiment
4DNEXI7YGDDI
Bio Rep 2, Tec Rep 1
PLAC-seq against H3K4me3 (mouse) on forebrain
File
Contact List-replicate (pairs)
4DNFI9DMRI53
99.89m
50.408%
19.898%
29.694%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNESS2HA1AN
Multiple Experiments
File
Contact Matrix (mcool)
4DNFIGDZCC4M
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
4DNEXEE5G2C7
Bio Rep 1, Tec Rep 1
PLAC-seq against H3K4me3 (mouse) on forebrain
File
Alignments (bam)
4DNFIIW9CYV1
351.52m
17.068%
14.908%
9.997%
4.688%
0.053%
Experiment
4DNEXI7YGDDI
Bio Rep 2, Tec Rep 1
PLAC-seq against H3K4me3 (mouse) on forebrain
File
Alignments (bam)
4DNFIPVYFZW3
183.76m
23.626%
9.917%
3.828%
8.27%
0.049%