ExperimentSetReplicate

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ExperimentSet4DNESR5QMPXM
released
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H3K4me3 PLAC-seq on C57BL/6NCrl embryonic day 12.5 mouse midbrain

   April 24th, 2022 at 12:20am
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 
midbrain
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
4DNESR5QMPXM
Multiple Experiments
File
4DNFIYX7FT84
contact list-combined (pairs)
5.07 GB
-
File
4DNFI8MKIUJU
contact matrix (hic)
2.93 GB
-
File
4DNFIHBKOMA6
contact matrix (mcool)
1.9 GB
Experiment
4DNEXDC96XE2
Bio Rep 1, Tec Rep 1
PLAC-seq against H3K4me3 (mouse) on midbrain
File
4DNFIKE3QAKR
alignments (bam)
24.35 GB
-
File
4DNFIPBDDS9C
contact list-replicate (pairs)
2.34 GB
-
Experiment
4DNEX8EOS5HK
Bio Rep 2, Tec Rep 1
PLAC-seq against H3K4me3 (mouse) on midbrain
File
4DNFIP45GIBA
alignments (bam)
32.58 GB
-
File
4DNFILSOBZU9
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
4DNESR5QMPXM
Multiple Experiments
File
Contact List-combined (pairs)
4DNFIYX7FT84
277.99m
48.107%
19.377%
32.516%
Experiment
4DNEXDC96XE2
Bio Rep 1, Tec Rep 1
PLAC-seq against H3K4me3 (mouse) on midbrain
File
Contact List-replicate (pairs)
4DNFIPBDDS9C
118.83m
48.583%
20.238%
31.178%
Experiment
4DNEX8EOS5HK
Bio Rep 2, Tec Rep 1
PLAC-seq against H3K4me3 (mouse) on midbrain
File
Contact List-replicate (pairs)
4DNFILSOBZU9
159.16m
47.752%
18.733%
33.515%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNESR5QMPXM
Multiple Experiments
File
Contact Matrix (mcool)
4DNFIHBKOMA6
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
4DNEXDC96XE2
Bio Rep 1, Tec Rep 1
PLAC-seq against H3K4me3 (mouse) on midbrain
File
Alignments (bam)
4DNFIKE3QAKR
194.28m
12.363%
18.331%
6.929%
1.213%
0.06%
Experiment
4DNEX8EOS5HK
Bio Rep 2, Tec Rep 1
PLAC-seq against H3K4me3 (mouse) on midbrain
File
Alignments (bam)
4DNFIP45GIBA
274.29m
12.081%
19.502%
9.438%
0.951%
0.066%