ExperimentSetReplicate

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ExperimentSet4DNES8DEXNEY
released
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H3K4me3 PLAC-seq on C57BL/6NCrl embryonic day 15.5 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., Nature structural & molecular biology 2024

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

    Explore Data

Loading
Experiment
File
File Type
File Size
Notes
From Multiple Experiments
4DNES8DEXNEY
Multiple Experiments
File
4DNFIRVIFLC6
contact list-combined (pairs)
4.25 GB
-
File
4DNFIZS5A9SQ
contact matrix (hic)
2.33 GB
-
File
4DNFI4K7KIYD
contact matrix (mcool)
1.5 GB
Experiment
4DNEXWK39FE7
Bio Rep 1, Tec Rep 1
PLAC-seq against H3K4me3 (mouse) on forebrain
File
4DNFIEQ77AZ6
alignments (bam)
17.86 GB
-
File
4DNFIPECU4ZE
contact list-replicate (pairs)
2.08 GB
-
Experiment
4DNEXQI3LA7A
Bio Rep 2, Tec Rep 1
PLAC-seq against H3K4me3 (mouse) on forebrain
File
4DNFIRL1PG9T
alignments (bam)
21.91 GB
-
File
4DNFI441R58O
contact list-replicate (pairs)
2.51 GB
-

Quality Metrics

Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Details
From Multiple Experiments
4DNES8DEXNEY
Multiple Experiments
File
Contact List-combined (pairs)
4DNFIRVIFLC6
234.96m
46.883%
24.0%
29.117%
Experiment
4DNEXWK39FE7
Bio Rep 1, Tec Rep 1
PLAC-seq against H3K4me3 (mouse) on forebrain
File
Contact List-replicate (pairs)
4DNFIPECU4ZE
105.71m
45.854%
22.795%
31.35%
Experiment
4DNEXQI3LA7A
Bio Rep 2, Tec Rep 1
PLAC-seq against H3K4me3 (mouse) on forebrain
File
Contact List-replicate (pairs)
4DNFI441R58O
129.25m
47.725%
24.985%
27.29%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNES8DEXNEY
Multiple Experiments
File
Contact Matrix (mcool)
4DNFI4K7KIYD
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
4DNEXWK39FE7
Bio Rep 1, Tec Rep 1
PLAC-seq against H3K4me3 (mouse) on forebrain
File
Alignments (bam)
4DNFIEQ77AZ6
161.36m
10.766%
17.07%
6.634%
0.015%
0.048%
Experiment
4DNEXQI3LA7A
Bio Rep 2, Tec Rep 1
PLAC-seq against H3K4me3 (mouse) on forebrain
File
Alignments (bam)
4DNFIRL1PG9T
195.23m
11.061%
17.15%
5.569%
0.017%
0.037%