ExperimentSetReplicate

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ExperimentSet4DNESXAK169L
released
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Biological replicates of Capture-C on commd3- G1E-ER4 cells in prometaphase

   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

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Experiment
File
File Type
File Size
Notes
From Multiple Experiments
4DNESXAK169L
Multiple Experiments
File
4DNFISFWXM3L
contact list-combined (pairs)
253.2 MB
-
File
4DNFI72IFZFC
contact matrix (hic)
79.61 MB
-
File
4DNFISOGGBVS
contact matrix (mcool)
47.47 MB
Experiment
4DNEXMFP37LZ
Bio Rep 1, Tec Rep 1
Capture Hi-C on G1E-ER4 with commd3 CTCF site deletion, mCherry-MD with DpnII
File
4DNFIRA2XXCR
alignments (bam)
2.89 GB
-
File
4DNFI4BP7U3V
contact list-replicate (pairs)
131.38 MB
-
Experiment
4DNEXHZFPIFW
Bio Rep 2, Tec Rep 1
Capture Hi-C on G1E-ER4 with commd3 CTCF site deletion, mCherry-MD with DpnII
File
4DNFIUWWL4WL
alignments (bam)
3.53 GB
-
File
4DNFIEWW7KJF
contact list-replicate (pairs)
127.53 MB
-

Quality Metrics

Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Details
From Multiple Experiments
4DNESXAK169L
Multiple Experiments
File
Contact List-combined (pairs)
4DNFISFWXM3L
19.96m
5.822%
92.452%
1.726%
Experiment
4DNEXMFP37LZ
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)
4DNFI4BP7U3V
10.12m
6.67%
91.595%
1.735%
Experiment
4DNEXHZFPIFW
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)
4DNFIEWW7KJF
9.84m
4.95%
93.333%
1.717%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNESXAK169L
Multiple Experiments
File
Contact Matrix (mcool)
4DNFISOGGBVS
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
4DNEXMFP37LZ
Bio Rep 1, Tec Rep 1
Capture Hi-C on G1E-ER4 with commd3 CTCF site deletion, mCherry-MD with DpnII
File
Alignments (bam)
4DNFIRA2XXCR
30.84m
2.911%
23.897%
39.462%
0.912%
0.076%
Experiment
4DNEXHZFPIFW
Bio Rep 2, Tec Rep 1
Capture Hi-C on G1E-ER4 with commd3 CTCF site deletion, mCherry-MD with DpnII
File
Alignments (bam)
4DNFIUWWL4WL
40.97m
2.807%
21.856%
50.627%
0.681%
0.054%