ExperimentSetReplicate

ExperimentSet4DNESV96LIGH
released
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H3K4me3 PLAC-seq on C57BL/6NCrl embryonic day 12.5 mouse neural tube

   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 
neural tube
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
4DNESV96LIGH
Multiple Experiments
File
Contact List-combined (pairs)
4DNFIM316MVE
225.82m
44.775%
34.1%
21.125%
Experiment
4DNEXI6DEG2D
Bio Rep 1, Tec Rep 1
PLAC-seq against H3K4me3 (mouse) on neural tube
File
Contact List-replicate (pairs)
4DNFIP8UZPS4
127.39m
38.85%
43.578%
17.572%
Experiment
4DNEXIJAMVNJ
Bio Rep 2, Tec Rep 1
PLAC-seq against H3K4me3 (mouse) on neural tube
File
Contact List-replicate (pairs)
4DNFIPGFTLML
98.43m
52.441%
21.834%
25.725%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNESV96LIGH
Multiple Experiments
File
Contact Matrix (mcool)
4DNFIISYZUOT
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
4DNEXI6DEG2D
Bio Rep 1, Tec Rep 1
PLAC-seq against H3K4me3 (mouse) on neural tube
File
Alignments (bam)
4DNFIG1UH7F6
234.38m
8.731%
20.2%
16.671%
0.047%
0.043%
Experiment
4DNEXIJAMVNJ
Bio Rep 2, Tec Rep 1
PLAC-seq against H3K4me3 (mouse) on neural tube
File
Alignments (bam)
4DNFI9CU42OB
160.25m
10.024%
19.962%
8.528%
0.059%
0.052%