ExperimentSetReplicate

ExperimentSet4DNESTLK5GLR
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H3K4me3 PLAC-seq on C57BL/6NCrl embryonic day 12.5 mouse craniofacial prominence

   April 24th, 2022 at 12:21am
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 
embryonic facial prominence
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
4DNESTLK5GLR
Multiple Experiments
File
Contact List-combined (pairs)
4DNFIGDZVDQS
235.07m
45.769%
20.933%
33.298%
Experiment
4DNEXXCA2HMY
Bio Rep 1, Tec Rep 1
PLAC-seq against H3K4me3 (mouse) on embryonic facial prominence
File
Contact List-replicate (pairs)
4DNFIHMUCVQ7
111.23m
46.343%
21.547%
32.109%
Experiment
4DNEXTOQ1WY2
Bio Rep 2, Tec Rep 1
PLAC-seq against H3K4me3 (mouse) on embryonic facial prominence
File
Contact List-replicate (pairs)
4DNFISDB9D1D
123.84m
45.253%
20.382%
34.366%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNESTLK5GLR
Multiple Experiments
File
Contact Matrix (mcool)
4DNFI2699TO1
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
4DNEXXCA2HMY
Bio Rep 1, Tec Rep 1
PLAC-seq against H3K4me3 (mouse) on embryonic facial prominence
File
Alignments (bam)
4DNFIRLVT91U
205.62m
11.891%
19.948%
14.02%
0.047%
0.093%
Experiment
4DNEXTOQ1WY2
Bio Rep 2, Tec Rep 1
PLAC-seq against H3K4me3 (mouse) on embryonic facial prominence
File
Alignments (bam)
4DNFIRV8O41I
205.49m
12.061%
19.799%
7.846%
0.027%
0.106%