ExperimentSetReplicate

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ExperimentSet4DNESS2HA1AN
released
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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., Nature structural & molecular biology 2024

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

    Explore Data

Loading
Experiment
File
File Type
File Size
Notes
From Multiple Experiments
4DNESS2HA1AN
Multiple Experiments
File
4DNFIIII16YT
contact list-combined (pairs)
5.26 GB
-
File
4DNFIG89V5T3
contact matrix (hic)
2.84 GB
-
File
4DNFIGDZCC4M
contact matrix (mcool)
1.85 GB
Experiment
4DNEXEE5G2C7
Bio Rep 1, Tec Rep 1
PLAC-seq against H3K4me3 (mouse) on forebrain
File
4DNFIIW9CYV1
alignments (bam)
57.11 GB
-
File
4DNFI7ONPRLV
contact list-replicate (pairs)
3.7 GB
-
Experiment
4DNEXI7YGDDI
Bio Rep 2, Tec Rep 1
PLAC-seq against H3K4me3 (mouse) on forebrain
File
4DNFIPVYFZW3
alignments (bam)
38.31 GB
-
File
4DNFI9DMRI53
contact list-replicate (pairs)
1.96 GB
-

Quality Metrics

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