ExperimentSetReplicate

ExperimentSet4DNES8DEXNEY
released
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H3K4me3 PLAC-seq on C57BL/6NCrl embryonic day 15.5 mouse forebrain

   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 
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
4DNES8DEXNEY
Multiple Experiments
File
Contact List-combined (pairs)
4DNFIRVIFLC6
234.96m
46.883%
24.0%
29.117%
Experiment
4DNEXWK39FE7
Bio Rep 1, Tec Rep 1
PLAC-seq against H3K4me3 (mouse) on forebrain
File
Contact List-replicate (pairs)
4DNFIPECU4ZE
105.71m
45.854%
22.795%
31.35%
Experiment
4DNEXQI3LA7A
Bio Rep 2, Tec Rep 1
PLAC-seq against H3K4me3 (mouse) on forebrain
File
Contact List-replicate (pairs)
4DNFI441R58O
129.25m
47.725%
24.985%
27.29%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNES8DEXNEY
Multiple Experiments
File
Contact Matrix (mcool)
4DNFI4K7KIYD
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
4DNEXWK39FE7
Bio Rep 1, Tec Rep 1
PLAC-seq against H3K4me3 (mouse) on forebrain
File
Alignments (bam)
4DNFIEQ77AZ6
161.36m
10.766%
17.07%
6.634%
0.015%
0.048%
Experiment
4DNEXQI3LA7A
Bio Rep 2, Tec Rep 1
PLAC-seq against H3K4me3 (mouse) on forebrain
File
Alignments (bam)
4DNFIRL1PG9T
195.23m
11.061%
17.15%
5.569%
0.017%
0.037%