ExperimentSetReplicate

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ExperimentSet4DNES853WOFN
released
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Biological replicates of Capture-C on G1E-ER4 cells in anaphase/telophase

   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
4DNES853WOFN
Multiple Experiments
File
4DNFIRU3IDE4
contact list-combined (pairs)
897.78 MB
-
File
4DNFIOCZBQ16
contact matrix (hic)
225.9 MB
-
File
4DNFI7FYKVFV
contact matrix (mcool)
123.67 MB
Experiment
4DNEXX63NJED
Bio Rep 1, Tec Rep 1
Capture Hi-C on G1E-ER4 with mCherry-MD with DpnII
File
4DNFIUMFEEXK
alignments (bam)
4.95 GB
-
File
4DNFILYS5AGZ
contact list-replicate (pairs)
235.05 MB
-
Experiment
4DNEXUZUHNGT
Bio Rep 2, Tec Rep 1
Capture Hi-C on G1E-ER4 with mCherry-MD with DpnII
File
4DNFIKU2TLX1
alignments (bam)
5.98 GB
-
File
4DNFI1HGY6DA
contact list-replicate (pairs)
314.77 MB
-
Experiment
4DNEXA24SMHJ
Bio Rep 3, Tec Rep 1
Capture Hi-C on G1E-ER4 with mCherry-MD with DpnII
File
4DNFIJ5AYY6W
alignments (bam)
7.78 GB
-
File
4DNFI5961E7C
contact list-replicate (pairs)
366.33 MB
-

Quality Metrics

Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Details
From Multiple Experiments
4DNES853WOFN
Multiple Experiments
File
Contact List-combined (pairs)
4DNFIRU3IDE4
71.11m
8.061%
89.892%
2.047%
Experiment
4DNEXX63NJED
Bio Rep 1, Tec Rep 1
Capture Hi-C on G1E-ER4 with mCherry-MD with DpnII
File
Contact List-replicate (pairs)
4DNFILYS5AGZ
18.22m
7.472%
90.627%
1.901%
Experiment
4DNEXUZUHNGT
Bio Rep 2, Tec Rep 1
Capture Hi-C on G1E-ER4 with mCherry-MD with DpnII
File
Contact List-replicate (pairs)
4DNFI1HGY6DA
24.36m
9.133%
88.831%
2.037%
Experiment
4DNEXA24SMHJ
Bio Rep 3, Tec Rep 1
Capture Hi-C on G1E-ER4 with mCherry-MD with DpnII
File
Contact List-replicate (pairs)
4DNFI5961E7C
28.53m
7.523%
90.329%
2.149%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNES853WOFN
Multiple Experiments
File
Contact Matrix (mcool)
4DNFI7FYKVFV
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
4DNEXX63NJED
Bio Rep 1, Tec Rep 1
Capture Hi-C on G1E-ER4 with mCherry-MD with DpnII
File
Alignments (bam)
4DNFIUMFEEXK
49.54m
3.668%
24.808%
33.573%
1.169%
0.076%
Experiment
4DNEXUZUHNGT
Bio Rep 2, Tec Rep 1
Capture Hi-C on G1E-ER4 with mCherry-MD with DpnII
File
Alignments (bam)
4DNFIKU2TLX1
57.39m
3.898%
24.945%
27.16%
1.55%
0.082%
Experiment
4DNEXA24SMHJ
Bio Rep 3, Tec Rep 1
Capture Hi-C on G1E-ER4 with mCherry-MD with DpnII
File
Alignments (bam)
4DNFIJ5AYY6W
79.84m
3.799%
23.002%
36.267%
1.198%
0.068%