ExperimentSetReplicate

Browser Suggestion

Google Chrome  or Mozilla Firefox are the recommended browser(s) for using the 4DN Data Portal.

Microsoft Edge, Safari, Opera etc. should work for a majority of portal functions but are not explicitly supported and may present some glitches, e.g. during submission.

ExperimentSet4DNESI6KY1VF
released
View JSON

Biological replicates of Capture-C on commd3- 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 commd3 CTCF site deletion, mCherry-MD
Experiment Type(s) 
Capture Hi-C
Modification Type 
None
Treatment Type 
Chemical
Assay Details 
Target: GRCm38:2:18672514-18673054 mouse region

7 Processed Files

    Explore Data

Loading
Experiment
File
File Type
File Size
Notes
From Multiple Experiments
4DNESI6KY1VF
Multiple Experiments
File
4DNFIO27ADLU
contact list-combined (pairs)
253.68 MB
-
File
4DNFIH3N65VK
contact matrix (hic)
71.41 MB
-
File
4DNFICQK4N8B
contact matrix (mcool)
39.16 MB
Experiment
4DNEXUCKWI3E
Bio Rep 1, Tec Rep 1
Capture Hi-C on G1E-ER4 with commd3 CTCF site deletion, mCherry-MD with DpnII
File
4DNFI2TYTHBU
alignments (bam)
2.84 GB
-
File
4DNFIHMNYBUX
contact list-replicate (pairs)
125.74 MB
-
Experiment
4DNEXHE1NNLH
Bio Rep 2, Tec Rep 1
Capture Hi-C on G1E-ER4 with commd3 CTCF site deletion, mCherry-MD with DpnII
File
4DNFIEQQCWRG
alignments (bam)
3.77 GB
-
File
4DNFIC1GNM7V
contact list-replicate (pairs)
133.07 MB
-

Quality Metrics

Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Details
From Multiple Experiments
4DNESI6KY1VF
Multiple Experiments
File
Contact List-combined (pairs)
4DNFIO27ADLU
20.35m
2.705%
95.505%
1.79%
Experiment
4DNEXUCKWI3E
Bio Rep 1, Tec Rep 1
Capture Hi-C on G1E-ER4 with commd3 CTCF site deletion, mCherry-MD with DpnII
File
Contact List-replicate (pairs)
4DNFIHMNYBUX
9.79m
4.381%
93.725%
1.894%
Experiment
4DNEXHE1NNLH
Bio Rep 2, Tec Rep 1
Capture Hi-C on G1E-ER4 with commd3 CTCF site deletion, mCherry-MD with DpnII
File
Contact List-replicate (pairs)
4DNFIC1GNM7V
10.56m
1.15%
97.155%
1.694%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNESI6KY1VF
Multiple Experiments
File
Contact Matrix (mcool)
4DNFICQK4N8B
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
4DNEXUCKWI3E
Bio Rep 1, Tec Rep 1
Capture Hi-C on G1E-ER4 with commd3 CTCF site deletion, mCherry-MD with DpnII
File
Alignments (bam)
4DNFI2TYTHBU
30.71m
2.811%
23.998%
40.563%
0.744%
0.072%
Experiment
4DNEXHE1NNLH
Bio Rep 2, Tec Rep 1
Capture Hi-C on G1E-ER4 with commd3 CTCF site deletion, mCherry-MD with DpnII
File
Alignments (bam)
4DNFIEQQCWRG
45.59m
2.356%
20.759%
53.401%
0.33%
0.054%