ExperimentSetReplicate

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., bioRxiv 2022

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

Quality Metrics

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