ExperimentSetReplicate

ExperimentSet4DNES2VIMAYW
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H3K4me3 PLAC-seq on C57BL/6NCrl embryonic day 13.5 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
4DNES2VIMAYW
Multiple Experiments
File
Contact List-combined (pairs)
4DNFIEGGJA7S
301.1m
45.489%
27.15%
27.362%
Experiment
4DNEXJVKEV2G
Bio Rep 1, Tec Rep 1
PLAC-seq against H3K4me3 (mouse) on forebrain
File
Contact List-replicate (pairs)
4DNFI4TTH728
155.48m
46.506%
23.035%
30.459%
Experiment
4DNEXBMGD9CJ
Bio Rep 2, Tec Rep 1
PLAC-seq against H3K4me3 (mouse) on forebrain
File
Contact List-replicate (pairs)
4DNFIZYII6EC
145.62m
44.403%
31.543%
24.054%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNES2VIMAYW
Multiple Experiments
File
Contact Matrix (mcool)
4DNFI717C3SY
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
4DNEXJVKEV2G
Bio Rep 1, Tec Rep 1
PLAC-seq against H3K4me3 (mouse) on forebrain
File
Alignments (bam)
4DNFIA2NDM4B
330.94m
14.425%
15.164%
18.673%
4.756%
0.042%
Experiment
4DNEXBMGD9CJ
Bio Rep 2, Tec Rep 1
PLAC-seq against H3K4me3 (mouse) on forebrain
File
Alignments (bam)
4DNFI8J8YLIR
281.35m
12.675%
17.28%
18.225%
0.062%
0.031%