ExperimentSetReplicate

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ExperimentSet4DNESO2R26BF
released
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H3K4me3 PLAC-seq on C57BL/6NCrl embryonic day 12.5 mouse hindbrain

   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., Nature structural & molecular biology 2024

Experiment Set Properties  

Set Type 
Replicate
Organism 
M. musculus
Sample Type 
tissue
Sample 
hindbrain
Experiment Type(s) 
PLAC-seq
Modification Type 
None
Treatment Type 
None
Assay Details 
Target: H3K4me3 (mouse)

7 Processed Files

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Experiment
File
File Type
File Size
Notes
From Multiple Experiments
4DNESO2R26BF
Multiple Experiments
File
4DNFIYRY47VW
contact list-combined (pairs)
5.53 GB
-
File
4DNFI8LSB7TU
contact matrix (hic)
3.02 GB
-
File
4DNFIIBPZFOJ
contact matrix (mcool)
1.96 GB
Experiment
4DNEXKX8ZV1G
Bio Rep 1, Tec Rep 1
PLAC-seq against H3K4me3 (mouse) on hindbrain
File
4DNFINSPXGXE
alignments (bam)
21.99 GB
-
File
4DNFIZQG6YFY
contact list-replicate (pairs)
2.38 GB
-
Experiment
4DNEXX6MZJ4P
Bio Rep 2, Tec Rep 1
PLAC-seq against H3K4me3 (mouse) on hindbrain
File
4DNFIXHP81MV
alignments (bam)
51.5 GB
-
File
4DNFI12RTVM1
contact list-replicate (pairs)
3.56 GB
-

Quality Metrics

Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Details
From Multiple Experiments
4DNESO2R26BF
Multiple Experiments
File
Contact List-combined (pairs)
4DNFIYRY47VW
298.12m
46.322%
21.661%
32.017%
Experiment
4DNEXKX8ZV1G
Bio Rep 1, Tec Rep 1
PLAC-seq against H3K4me3 (mouse) on hindbrain
File
Contact List-replicate (pairs)
4DNFIZQG6YFY
120.72m
44.962%
23.164%
31.874%
Experiment
4DNEXX6MZJ4P
Bio Rep 2, Tec Rep 1
PLAC-seq against H3K4me3 (mouse) on hindbrain
File
Contact List-replicate (pairs)
4DNFI12RTVM1
177.41m
47.248%
20.638%
32.114%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNESO2R26BF
Multiple Experiments
File
Contact Matrix (mcool)
4DNFIIBPZFOJ
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
4DNEXKX8ZV1G
Bio Rep 1, Tec Rep 1
PLAC-seq against H3K4me3 (mouse) on hindbrain
File
Alignments (bam)
4DNFINSPXGXE
199.94m
11.397%
18.717%
9.484%
0.028%
0.083%
Experiment
4DNEXX6MZJ4P
Bio Rep 2, Tec Rep 1
PLAC-seq against H3K4me3 (mouse) on hindbrain
File
Alignments (bam)
4DNFIXHP81MV
292.21m
15.205%
15.561%
4.09%
4.432%
0.078%