ExperimentSetReplicate

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ExperimentSet4DNESV96LIGH
released
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H3K4me3 PLAC-seq on C57BL/6NCrl embryonic day 12.5 mouse neural tube

   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 
neural tube
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
4DNESV96LIGH
Multiple Experiments
File
4DNFIM316MVE
contact list-combined (pairs)
3.94 GB
-
File
4DNFIC5CBUJB
contact matrix (hic)
1.96 GB
-
File
4DNFIISYZUOT
contact matrix (mcool)
1.25 GB
Experiment
4DNEXI6DEG2D
Bio Rep 1, Tec Rep 1
PLAC-seq against H3K4me3 (mouse) on neural tube
File
4DNFIG1UH7F6
alignments (bam)
22.62 GB
-
File
4DNFIP8UZPS4
contact list-replicate (pairs)
2.38 GB
-
Experiment
4DNEXIJAMVNJ
Bio Rep 2, Tec Rep 1
PLAC-seq against H3K4me3 (mouse) on neural tube
File
4DNFI9CU42OB
alignments (bam)
16.19 GB
-
File
4DNFIPGFTLML
contact list-replicate (pairs)
1.86 GB
-

Quality Metrics

Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Details
From Multiple Experiments
4DNESV96LIGH
Multiple Experiments
File
Contact List-combined (pairs)
4DNFIM316MVE
225.82m
44.775%
34.1%
21.125%
Experiment
4DNEXI6DEG2D
Bio Rep 1, Tec Rep 1
PLAC-seq against H3K4me3 (mouse) on neural tube
File
Contact List-replicate (pairs)
4DNFIP8UZPS4
127.39m
38.85%
43.578%
17.572%
Experiment
4DNEXIJAMVNJ
Bio Rep 2, Tec Rep 1
PLAC-seq against H3K4me3 (mouse) on neural tube
File
Contact List-replicate (pairs)
4DNFIPGFTLML
98.43m
52.441%
21.834%
25.725%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNESV96LIGH
Multiple Experiments
File
Contact Matrix (mcool)
4DNFIISYZUOT
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
4DNEXI6DEG2D
Bio Rep 1, Tec Rep 1
PLAC-seq against H3K4me3 (mouse) on neural tube
File
Alignments (bam)
4DNFIG1UH7F6
234.38m
8.731%
20.2%
16.671%
0.047%
0.043%
Experiment
4DNEXIJAMVNJ
Bio Rep 2, Tec Rep 1
PLAC-seq against H3K4me3 (mouse) on neural tube
File
Alignments (bam)
4DNFI9CU42OB
160.25m
10.024%
19.962%
8.528%
0.059%
0.052%