ExperimentSetReplicate

ExperimentSet4DNES8IEZPCJ
released
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H3K4me3 PLAC-seq on C57BL/6NCrl embryonic day 16.5 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
4DNES8IEZPCJ
Multiple Experiments
File
Contact List-combined (pairs)
4DNFIGQP2AXF
232.26m
49.554%
23.675%
26.771%
Experiment
4DNEXLJ6ILQ4
Bio Rep 1, Tec Rep 1
PLAC-seq against H3K4me3 (mouse) on forebrain
File
Contact List-replicate (pairs)
4DNFITPZX4FU
124.71m
50.235%
19.731%
30.034%
Experiment
4DNEX4GYFTOX
Bio Rep 2, Tec Rep 1
PLAC-seq against H3K4me3 (mouse) on forebrain
File
Contact List-replicate (pairs)
4DNFIN4CDKJS
107.55m
48.765%
28.248%
22.987%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNES8IEZPCJ
Multiple Experiments
File
Contact Matrix (mcool)
4DNFIOFW5AE4
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
4DNEXLJ6ILQ4
Bio Rep 1, Tec Rep 1
PLAC-seq against H3K4me3 (mouse) on forebrain
File
Alignments (bam)
4DNFIOJMU2IN
198.17m
17.358%
9.762%
3.024%
6.926%
0.041%
Experiment
4DNEX4GYFTOX
Bio Rep 2, Tec Rep 1
PLAC-seq against H3K4me3 (mouse) on forebrain
File
Alignments (bam)
4DNFIHHDLEVR
169.76m
11.072%
16.988%
8.543%
0.046%
0.026%