ExperimentSetReplicate

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ExperimentSet4DNESP54RGT7
released
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Biological replicates of Capture-C on G1E-ER4 cells in early 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
4DNESP54RGT7
Multiple Experiments
File
4DNFISYYUZEY
contact list-combined (pairs)
791.32 MB
-
File
4DNFI2NLDKXV
contact matrix (hic)
198.93 MB
-
File
4DNFIUP7YIRP
contact matrix (mcool)
109.22 MB
Experiment
4DNEXJO9TIX3
Bio Rep 1, Tec Rep 1
Capture Hi-C on G1E-ER4 with mCherry-MD with DpnII
File
4DNFIPEUNPJI
alignments (bam)
4.41 GB
-
File
4DNFIGSU6FST
contact list-replicate (pairs)
201.87 MB
-
Experiment
4DNEXPDY1DXS
Bio Rep 2, Tec Rep 1
Capture Hi-C on G1E-ER4 with mCherry-MD with DpnII
File
4DNFIABBN77Z
alignments (bam)
5.9 GB
-
File
4DNFIHTYYVJD
contact list-replicate (pairs)
318.1 MB
-
Experiment
4DNEXK3SANY4
Bio Rep 3, Tec Rep 1
Capture Hi-C on G1E-ER4 with mCherry-MD with DpnII
File
4DNFIN7BKBUX
alignments (bam)
6.51 GB
-
File
4DNFIZV22CDV
contact list-replicate (pairs)
287.7 MB
-

Quality Metrics

Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Details
From Multiple Experiments
4DNESP54RGT7
Multiple Experiments
File
Contact List-combined (pairs)
4DNFISYYUZEY
62.68m
7.54%
90.414%
2.047%
Experiment
4DNEXJO9TIX3
Bio Rep 1, Tec Rep 1
Capture Hi-C on G1E-ER4 with mCherry-MD with DpnII
File
Contact List-replicate (pairs)
4DNFIGSU6FST
15.62m
7.29%
90.713%
1.997%
Experiment
4DNEXPDY1DXS
Bio Rep 2, Tec Rep 1
Capture Hi-C on G1E-ER4 with mCherry-MD with DpnII
File
Contact List-replicate (pairs)
4DNFIHTYYVJD
24.82m
6.936%
91.123%
1.941%
Experiment
4DNEXK3SANY4
Bio Rep 3, Tec Rep 1
Capture Hi-C on G1E-ER4 with mCherry-MD with DpnII
File
Contact List-replicate (pairs)
4DNFIZV22CDV
22.25m
8.388%
89.412%
2.2%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNESP54RGT7
Multiple Experiments
File
Contact Matrix (mcool)
4DNFIUP7YIRP
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
4DNEXJO9TIX3
Bio Rep 1, Tec Rep 1
Capture Hi-C on G1E-ER4 with mCherry-MD with DpnII
File
Alignments (bam)
4DNFIPEUNPJI
43.19m
4.064%
24.165%
34.389%
1.22%
0.078%
Experiment
4DNEXPDY1DXS
Bio Rep 2, Tec Rep 1
Capture Hi-C on G1E-ER4 with mCherry-MD with DpnII
File
Alignments (bam)
4DNFIABBN77Z
57.97m
3.572%
23.029%
29.346%
1.243%
0.08%
Experiment
4DNEXK3SANY4
Bio Rep 3, Tec Rep 1
Capture Hi-C on G1E-ER4 with mCherry-MD with DpnII
File
Alignments (bam)
4DNFIN7BKBUX
64.67m
4.348%
22.887%
37.05%
1.313%
0.071%