ExperimentSetReplicate

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ExperimentSet4DNESU5FZUIT
released
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Biological replicates of Capture-C on 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 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

    Explore Data

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Experiment
File
File Type
File Size
Notes
From Multiple Experiments
4DNESU5FZUIT
Multiple Experiments
File
4DNFITEOUJIQ
contact list-combined (pairs)
899.03 MB
-
File
4DNFIRV7KUOW
contact matrix (hic)
211.16 MB
-
File
4DNFIJU6DXJ4
contact matrix (mcool)
119.38 MB
Experiment
4DNEX9AXY1YT
Bio Rep 1, Tec Rep 1
Capture Hi-C on G1E-ER4 with mCherry-MD with DpnII
File
4DNFI6B2UU2U
alignments (bam)
6.37 GB
-
File
4DNFIDFZ4T75
contact list-replicate (pairs)
297.8 MB
-
Experiment
4DNEXNR4X9FC
Bio Rep 2, Tec Rep 1
Capture Hi-C on G1E-ER4 with mCherry-MD with DpnII
File
4DNFIVLSNEME
alignments (bam)
5.89 GB
-
File
4DNFIZ7EO798
contact list-replicate (pairs)
302.16 MB
-
Experiment
4DNEXTLZ7XQM
Bio Rep 3, Tec Rep 1
Capture Hi-C on G1E-ER4 with mCherry-MD with DpnII
File
4DNFIX1IVUZT
alignments (bam)
7.02 GB
-
File
4DNFIDGHF1B6
contact list-replicate (pairs)
318.07 MB
-

Quality Metrics

Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Details
From Multiple Experiments
4DNESU5FZUIT
Multiple Experiments
File
Contact List-combined (pairs)
4DNFITEOUJIQ
71.3m
8.764%
89.506%
1.73%
Experiment
4DNEX9AXY1YT
Bio Rep 1, Tec Rep 1
Capture Hi-C on G1E-ER4 with mCherry-MD with DpnII
File
Contact List-replicate (pairs)
4DNFIDFZ4T75
23.06m
8.664%
89.334%
2.002%
Experiment
4DNEXNR4X9FC
Bio Rep 2, Tec Rep 1
Capture Hi-C on G1E-ER4 with mCherry-MD with DpnII
File
Contact List-replicate (pairs)
4DNFIZ7EO798
23.5m
8.771%
89.622%
1.607%
Experiment
4DNEXTLZ7XQM
Bio Rep 3, Tec Rep 1
Capture Hi-C on G1E-ER4 with mCherry-MD with DpnII
File
Contact List-replicate (pairs)
4DNFIDGHF1B6
24.74m
8.85%
89.558%
1.592%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNESU5FZUIT
Multiple Experiments
File
Contact Matrix (mcool)
4DNFIJU6DXJ4
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
4DNEX9AXY1YT
Bio Rep 1, Tec Rep 1
Capture Hi-C on G1E-ER4 with mCherry-MD with DpnII
File
Alignments (bam)
4DNFI6B2UU2U
63.94m
3.789%
26.138%
32.767%
1.244%
0.078%
Experiment
4DNEXNR4X9FC
Bio Rep 2, Tec Rep 1
Capture Hi-C on G1E-ER4 with mCherry-MD with DpnII
File
Alignments (bam)
4DNFIVLSNEME
58.23m
3.705%
24.825%
29.775%
1.329%
0.082%
Experiment
4DNEXTLZ7XQM
Bio Rep 3, Tec Rep 1
Capture Hi-C on G1E-ER4 with mCherry-MD with DpnII
File
Alignments (bam)
4DNFIX1IVUZT
72.62m
3.86%
24.391%
36.489%
1.196%
0.07%