ExperimentSetReplicate

ExperimentSet4DNESO2R26BF
released
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H3K4me3 PLAC-seq on C57BL/6NCrl embryonic day 12.5 mouse hindbrain

   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 
hindbrain
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
4DNESO2R26BF
Multiple Experiments
File
Contact List-combined (pairs)
4DNFIYRY47VW
298.12m
46.322%
21.661%
32.017%
Experiment
4DNEXKX8ZV1G
Bio Rep 1, Tec Rep 1
PLAC-seq against H3K4me3 (mouse) on hindbrain
File
Contact List-replicate (pairs)
4DNFIZQG6YFY
120.72m
44.962%
23.164%
31.874%
Experiment
4DNEXX6MZJ4P
Bio Rep 2, Tec Rep 1
PLAC-seq against H3K4me3 (mouse) on hindbrain
File
Contact List-replicate (pairs)
4DNFI12RTVM1
177.41m
47.248%
20.638%
32.114%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNESO2R26BF
Multiple Experiments
File
Contact Matrix (mcool)
4DNFIIBPZFOJ
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
4DNEXKX8ZV1G
Bio Rep 1, Tec Rep 1
PLAC-seq against H3K4me3 (mouse) on hindbrain
File
Alignments (bam)
4DNFINSPXGXE
199.94m
11.397%
18.717%
9.484%
0.028%
0.083%
Experiment
4DNEXX6MZJ4P
Bio Rep 2, Tec Rep 1
PLAC-seq against H3K4me3 (mouse) on hindbrain
File
Alignments (bam)
4DNFIXHP81MV
292.21m
15.205%
15.561%
4.09%
4.432%
0.078%