ExperimentSetReplicate

ExperimentSet4DNESR5QMPXM
released
View JSON

H3K4me3 PLAC-seq on C57BL/6NCrl embryonic day 12.5 mouse midbrain

   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 
midbrain
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
4DNESR5QMPXM
Multiple Experiments
File
Contact List-combined (pairs)
4DNFIYX7FT84
277.99m
48.107%
19.377%
32.516%
Experiment
4DNEXDC96XE2
Bio Rep 1, Tec Rep 1
PLAC-seq against H3K4me3 (mouse) on midbrain
File
Contact List-replicate (pairs)
4DNFIPBDDS9C
118.83m
48.583%
20.238%
31.178%
Experiment
4DNEX8EOS5HK
Bio Rep 2, Tec Rep 1
PLAC-seq against H3K4me3 (mouse) on midbrain
File
Contact List-replicate (pairs)
4DNFILSOBZU9
159.16m
47.752%
18.733%
33.515%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNESR5QMPXM
Multiple Experiments
File
Contact Matrix (mcool)
4DNFIHBKOMA6
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
4DNEXDC96XE2
Bio Rep 1, Tec Rep 1
PLAC-seq against H3K4me3 (mouse) on midbrain
File
Alignments (bam)
4DNFIKE3QAKR
194.28m
12.363%
18.331%
6.929%
1.213%
0.06%
Experiment
4DNEX8EOS5HK
Bio Rep 2, Tec Rep 1
PLAC-seq against H3K4me3 (mouse) on midbrain
File
Alignments (bam)
4DNFIP45GIBA
274.29m
12.081%
19.502%
9.438%
0.951%
0.066%