ExperimentSetReplicate

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ExperimentSet4DNESGAQJIF8
released
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H3K4me3 PLAC-seq on C57BL/6NCrl embryonic day 12.5 mouse forebrain

   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 
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
4DNESGAQJIF8
Multiple Experiments
File
4DNFIWP46MU4
contact list-combined (pairs)
4.58 GB
-
File
4DNFI7K1M7AG
contact matrix (hic)
2.39 GB
-
File
4DNFIMF7SWUU
contact matrix (mcool)
1.54 GB
Experiment
4DNEXRKUMDSN
Bio Rep 1, Tec Rep 1
PLAC-seq against H3K4me3 (mouse) on forebrain
File
4DNFIDDBMQJ9
alignments (bam)
43.61 GB
-
File
4DNFIEQTIO43
contact list-replicate (pairs)
2.32 GB
-
Experiment
4DNEXNS39Z9B
Bio Rep 2, Tec Rep 1
PLAC-seq against H3K4me3 (mouse) on forebrain
File
4DNFIOGK2BIL
alignments (bam)
32.86 GB
-
File
4DNFIRQJIWWT
contact list-replicate (pairs)
2.53 GB
-

Quality Metrics

Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Details
From Multiple Experiments
4DNESGAQJIF8
Multiple Experiments
File
Contact List-combined (pairs)
4DNFIWP46MU4
250.81m
43.717%
29.659%
26.624%
Experiment
4DNEXRKUMDSN
Bio Rep 1, Tec Rep 1
PLAC-seq against H3K4me3 (mouse) on forebrain
File
Contact List-replicate (pairs)
4DNFIEQTIO43
119.74m
50.584%
19.026%
30.39%
Experiment
4DNEXNS39Z9B
Bio Rep 2, Tec Rep 1
PLAC-seq against H3K4me3 (mouse) on forebrain
File
Contact List-replicate (pairs)
4DNFIRQJIWWT
131.07m
37.444%
39.373%
23.183%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNESGAQJIF8
Multiple Experiments
File
Contact Matrix (mcool)
4DNFIMF7SWUU
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
4DNEXRKUMDSN
Bio Rep 1, Tec Rep 1
PLAC-seq against H3K4me3 (mouse) on forebrain
File
Alignments (bam)
4DNFIDDBMQJ9
202.53m
19.228%
11.146%
3.169%
7.334%
0.066%
Experiment
4DNEXNS39Z9B
Bio Rep 2, Tec Rep 1
PLAC-seq against H3K4me3 (mouse) on forebrain
File
Alignments (bam)
4DNFIOGK2BIL
206.49m
10.104%
12.956%
9.764%
3.699%
0.045%