ExperimentSetReplicate

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ExperimentSet4DNESG7Q6HPT
released
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H3K4me3 PLAC-seq on C57BL/6NTac;6NCrl/Lap postnatal day 0 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
4DNESG7Q6HPT
Multiple Experiments
File
4DNFIP9RN8UE
contact list-combined (pairs)
4.03 GB
-
File
4DNFICXCS7LM
contact matrix (hic)
2.11 GB
-
File
4DNFIKXLY48D
contact matrix (mcool)
1.36 GB
Experiment
4DNEX6S3ZPB8
Bio Rep 1, Tec Rep 1
PLAC-seq against H3K4me3 (mouse) on forebrain
File
4DNFIWPENZKS
alignments (bam)
22.61 GB
-
File
4DNFIYJU7LUA
contact list-replicate (pairs)
2.38 GB
-
Experiment
4DNEXG8E8EZE
Bio Rep 2, Tec Rep 1
PLAC-seq against H3K4me3 (mouse) on forebrain
File
4DNFIE12PITF
alignments (bam)
18.43 GB
-
File
4DNFIQ4H9ODY
contact list-replicate (pairs)
1.97 GB
-

Quality Metrics

Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Details
From Multiple Experiments
4DNESG7Q6HPT
Multiple Experiments
File
Contact List-combined (pairs)
4DNFIP9RN8UE
231.5m
51.009%
24.498%
24.493%
Experiment
4DNEX6S3ZPB8
Bio Rep 1, Tec Rep 1
PLAC-seq against H3K4me3 (mouse) on forebrain
File
Contact List-replicate (pairs)
4DNFIYJU7LUA
126.45m
51.837%
22.932%
25.231%
Experiment
4DNEXG8E8EZE
Bio Rep 2, Tec Rep 1
PLAC-seq against H3K4me3 (mouse) on forebrain
File
Contact List-replicate (pairs)
4DNFIQ4H9ODY
105.05m
50.011%
26.383%
23.606%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNESG7Q6HPT
Multiple Experiments
File
Contact Matrix (mcool)
4DNFIKXLY48D
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
4DNEX6S3ZPB8
Bio Rep 1, Tec Rep 1
PLAC-seq against H3K4me3 (mouse) on forebrain
File
Alignments (bam)
4DNFIWPENZKS
207.02m
16.114%
17.541%
5.211%
0.053%
0.049%
Experiment
4DNEXG8E8EZE
Bio Rep 2, Tec Rep 1
PLAC-seq against H3K4me3 (mouse) on forebrain
File
Alignments (bam)
4DNFIE12PITF
171.49m
15.108%
16.663%
6.924%
0.05%
0.031%