ExperimentSetReplicate

ExperimentSet4DNESNQNNTDM
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Biological replicates of Capture-C on commd3- 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 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

Quality Metrics

Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Report
Details
From Multiple Experiments
4DNESNQNNTDM
Multiple Experiments
File
Contact List-combined (pairs)
4DNFI5P9ARPE
21.5m
4.322%
93.874%
1.804%
Experiment
4DNEXZCWIF7M
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)
4DNFIC7OOS4F
11.07m
5.388%
92.753%
1.859%
Experiment
4DNEXHFRGKKI
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)
4DNFI9WS7CCH
10.43m
3.19%
95.065%
1.745%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNESNQNNTDM
Multiple Experiments
File
Contact Matrix (mcool)
4DNFICC1E96C
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
4DNEXZCWIF7M
Bio Rep 1, Tec Rep 1
Capture Hi-C on G1E-ER4 with commd3 CTCF site deletion, mCherry-MD with DpnII
File
Alignments (bam)
4DNFIZYY99KS
31.61m
2.917%
25.228%
35.937%
0.885%
0.079%
Experiment
4DNEXHFRGKKI
Bio Rep 2, Tec Rep 1
Capture Hi-C on G1E-ER4 with commd3 CTCF site deletion, mCherry-MD with DpnII
File
Alignments (bam)
4DNFIKGTU1FI
41.24m
2.626%
22.232%
49.277%
0.575%
0.055%