ExperimentSetReplicate

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ExperimentSet4DNESSDAAS6D
released
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Biological replicates of Capture-C on G1E-ER4 cells in mid-G1 phase

   March 3rd, 2020 at 8:07pm
Source Publication
Chromatin structure dynamics during the mitosis-to-G1 phase transition.
Zhang H, Emerson DJ, et al., Nature 2019

Experiment Set Properties  

Set Type 
Replicate
Organism 
M. musculus
Sample Type 
stem cells
Sample 
G1E-ER4 with mCherry-MD
Experiment Type(s) 
Capture Hi-C
Modification Type 
None
Treatment Type 
Chemical
Assay Details 
Target: GRCm38:14:26669326-26669570 mouse region, GRCm38:16:93830868-93831393 mouse region, GRCm38:1:50962112-50962982 mouse region, GRCm38:2:167684388-167685405 mouse region, GRCm38:2:18672514-18673054 mouse region

9 Processed Files

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Experiment
File
File Type
File Size
Notes
From Multiple Experiments
4DNESSDAAS6D
Multiple Experiments
File
4DNFIA15GE6S
contact list-combined (pairs)
863.07 MB
-
File
4DNFI3SDZFCJ
contact matrix (hic)
212.93 MB
-
File
4DNFIFQJ9CDY
contact matrix (mcool)
115.3 MB
Experiment
4DNEX9VFHDXZ
Bio Rep 1, Tec Rep 1
Capture Hi-C on G1E-ER4 with mCherry-MD with DpnII
File
4DNFILQHHDSU
alignments (bam)
5.78 GB
-
File
4DNFIA9IE59A
contact list-replicate (pairs)
266.67 MB
-
Experiment
4DNEX7QBSBL2
Bio Rep 2, Tec Rep 1
Capture Hi-C on G1E-ER4 with mCherry-MD with DpnII
File
4DNFIXXLQWFP
alignments (bam)
5.38 GB
-
File
4DNFIMHXIFX7
contact list-replicate (pairs)
295.46 MB
-
Experiment
4DNEXGYKDKPM
Bio Rep 3, Tec Rep 1
Capture Hi-C on G1E-ER4 with mCherry-MD with DpnII
File
4DNFICQ33VUH
alignments (bam)
6.73 GB
-
File
4DNFIM2FHPUE
contact list-replicate (pairs)
320.13 MB
-

Quality Metrics

Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Details
From Multiple Experiments
4DNESSDAAS6D
Multiple Experiments
File
Contact List-combined (pairs)
4DNFIA15GE6S
68.53m
7.4%
90.44%
2.16%
Experiment
4DNEX9VFHDXZ
Bio Rep 1, Tec Rep 1
Capture Hi-C on G1E-ER4 with mCherry-MD with DpnII
File
Contact List-replicate (pairs)
4DNFIA9IE59A
20.64m
7.958%
89.718%
2.324%
Experiment
4DNEX7QBSBL2
Bio Rep 2, Tec Rep 1
Capture Hi-C on G1E-ER4 with mCherry-MD with DpnII
File
Contact List-replicate (pairs)
4DNFIMHXIFX7
23.13m
5.595%
92.571%
1.834%
Experiment
4DNEXGYKDKPM
Bio Rep 3, Tec Rep 1
Capture Hi-C on G1E-ER4 with mCherry-MD with DpnII
File
Contact List-replicate (pairs)
4DNFIM2FHPUE
24.76m
8.621%
89.052%
2.328%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNESSDAAS6D
Multiple Experiments
File
Contact Matrix (mcool)
4DNFIFQJ9CDY
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
4DNEX9VFHDXZ
Bio Rep 1, Tec Rep 1
Capture Hi-C on G1E-ER4 with mCherry-MD with DpnII
File
Alignments (bam)
4DNFILQHHDSU
59.26m
3.834%
22.88%
37.17%
1.289%
0.07%
Experiment
4DNEX7QBSBL2
Bio Rep 2, Tec Rep 1
Capture Hi-C on G1E-ER4 with mCherry-MD with DpnII
File
Alignments (bam)
4DNFIXXLQWFP
52.79m
3.365%
22.731%
29.028%
1.063%
0.079%
Experiment
4DNEXGYKDKPM
Bio Rep 3, Tec Rep 1
Capture Hi-C on G1E-ER4 with mCherry-MD with DpnII
File
Alignments (bam)
4DNFICQ33VUH
67.56m
3.962%
23.838%
34.077%
1.472%
0.071%