ExperimentSetReplicate

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ExperimentSet4DNESBUE56SA
released
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H3K4me3 PLAC-seq on C57BL/6NCrl embryonic day 12.5 mouse limb

   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 
limb
Experiment Type(s) 
PLAC-seq
Modification Type 
None
Treatment Type 
None
Assay Details 
Target: H3K4me3 (mouse)

7 Processed Files

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Loading
Experiment
File
File Type
File Size
Notes
From Multiple Experiments
4DNESBUE56SA
Multiple Experiments
File
4DNFI3CZGXLE
contact list-combined (pairs)
4.8 GB
-
File
4DNFIM9WGRWF
contact matrix (hic)
2.72 GB
-
File
4DNFIEIJZ244
contact matrix (mcool)
1.78 GB
Experiment
4DNEX7NAHTRI
Bio Rep 1, Tec Rep 1
PLAC-seq against H3K4me3 (mouse) on limb
File
4DNFICJZ8KB1
alignments (bam)
25.98 GB
-
File
4DNFI9JALLPX
contact list-replicate (pairs)
2.76 GB
-
Experiment
4DNEXER93ZRM
Bio Rep 2, Tec Rep 1
PLAC-seq against H3K4me3 (mouse) on limb
File
4DNFIV7XHY6L
alignments (bam)
22.61 GB
-
File
4DNFIP1OWX8L
contact list-replicate (pairs)
2.41 GB
-

Quality Metrics

Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Details
From Multiple Experiments
4DNESBUE56SA
Multiple Experiments
File
Contact List-combined (pairs)
4DNFI3CZGXLE
274.54m
53.924%
20.323%
25.752%
Experiment
4DNEX7NAHTRI
Bio Rep 1, Tec Rep 1
PLAC-seq against H3K4me3 (mouse) on limb
File
Contact List-replicate (pairs)
4DNFI9JALLPX
146.15m
53.74%
19.415%
26.845%
Experiment
4DNEXER93ZRM
Bio Rep 2, Tec Rep 1
PLAC-seq against H3K4me3 (mouse) on limb
File
Contact List-replicate (pairs)
4DNFIP1OWX8L
128.39m
54.134%
21.357%
24.509%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNESBUE56SA
Multiple Experiments
File
Contact Matrix (mcool)
4DNFIEIJZ244
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
4DNEX7NAHTRI
Bio Rep 1, Tec Rep 1
PLAC-seq against H3K4me3 (mouse) on limb
File
Alignments (bam)
4DNFICJZ8KB1
248.57m
9.672%
23.995%
7.455%
0.081%
0.064%
Experiment
4DNEXER93ZRM
Bio Rep 2, Tec Rep 1
PLAC-seq against H3K4me3 (mouse) on limb
File
Alignments (bam)
4DNFIV7XHY6L
217.66m
10.109%
23.038%
7.784%
0.082%
0.067%