ExperimentSetReplicate

ExperimentSet4DNESG7Q6HPT
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H3K4me3 PLAC-seq on C57BL/6NTac;6NCrl/Lap postnatal day 0 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
4DNESG7Q6HPT
Multiple Experiments
File
Contact List-combined (pairs)
4DNFIP9RN8UE
231.5m
51.009%
24.498%
24.493%
Experiment
4DNEX6S3ZPB8
Bio Rep 1, Tec Rep 1
PLAC-seq against H3K4me3 (mouse) on forebrain
File
Contact List-replicate (pairs)
4DNFIYJU7LUA
126.45m
51.837%
22.932%
25.231%
Experiment
4DNEXG8E8EZE
Bio Rep 2, Tec Rep 1
PLAC-seq against H3K4me3 (mouse) on forebrain
File
Contact List-replicate (pairs)
4DNFIQ4H9ODY
105.05m
50.011%
26.383%
23.606%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNESG7Q6HPT
Multiple Experiments
File
Contact Matrix (mcool)
4DNFIKXLY48D
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
4DNEX6S3ZPB8
Bio Rep 1, Tec Rep 1
PLAC-seq against H3K4me3 (mouse) on forebrain
File
Alignments (bam)
4DNFIWPENZKS
207.02m
16.114%
17.541%
5.211%
0.053%
0.049%
Experiment
4DNEXG8E8EZE
Bio Rep 2, Tec Rep 1
PLAC-seq against H3K4me3 (mouse) on forebrain
File
Alignments (bam)
4DNFIE12PITF
171.49m
15.108%
16.663%
6.924%
0.05%
0.031%