ExperimentSetReplicate

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ExperimentSet4DNES2VIMAYW
released
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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., 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
4DNES2VIMAYW
Multiple Experiments
File
4DNFIEGGJA7S
contact list-combined (pairs)
5.43 GB
-
File
4DNFIPXPQJR7
contact matrix (hic)
2.79 GB
-
File
4DNFI717C3SY
contact matrix (mcool)
1.82 GB
Experiment
4DNEXJVKEV2G
Bio Rep 1, Tec Rep 1
PLAC-seq against H3K4me3 (mouse) on forebrain
File
4DNFIA2NDM4B
alignments (bam)
52.26 GB
-
File
4DNFI4TTH728
contact list-replicate (pairs)
3.05 GB
-
Experiment
4DNEXBMGD9CJ
Bio Rep 2, Tec Rep 1
PLAC-seq against H3K4me3 (mouse) on forebrain
File
4DNFI8J8YLIR
alignments (bam)
28.95 GB
-
File
4DNFIZYII6EC
contact list-replicate (pairs)
2.77 GB
-

Quality Metrics

Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
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%