ExperimentSetReplicate

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., bioRxiv 2022

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

Quality Metrics

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