ExperimentSetReplicate

ExperimentSet4DNES6FARLK8
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dilution Hi-C on CAPH2-mAID cells in prometaphase (15m post G2 block, CAPH2-)

   October 30th, 2018 at 2:37pm
Source Publication
A pathway for mitotic chromosome formation.
Gibcus JH, Samejima K, et al., Science (New York, N.Y.) 2018

Assay Description  

Note on Processed Files  

Some annotated bam and pairs files generated in this Experiment Set may contain distinct reads that share the same identifier. This was caused by merging fastq files with integer identifiers (eg. @1, @2) during processing.

Experiment Set Properties  

Set Type 
Replicate
Organism 
G. gallus
Sample Type 
immortalized cells
Sample 
DT40 with random integration of GFP and AID-tagged CAP-H2 gene, NCAPH2 disruption, random integration of X. laevis Cdk1, CDK1 disruption
Experiment Type(s) 
Dilution Hi-C
Modification Type 
None
Treatment Type 
Chemical
Assay Details 
Enzyme: HindIII

10 Processed Files

Quality Metrics

Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Report
Details
From Multiple Experiments
4DNES6FARLK8
Multiple Experiments
File
Contact List-combined (pairs)
4DNFIEELQ6XE
238.81m
45.194%
31.44%
23.366%
Experiment
4DNEXBJKTWVH
Bio Rep 1, Tec Rep 1
Dilution Hi-C on DT40 with random integration of GFP and AID-tagged CAP-H2 gene, NCAPH2 disruption, random integration of X. laevis Cdk1, CDK1 disruption with HindIII
File
Contact List-replicate (pairs)
4DNFITSRGCJ7
34.16m
4.568%
92.52%
2.912%
Experiment
4DNEX61FZW4H
Bio Rep 2, Tec Rep 1
Dilution Hi-C on DT40 with random integration of GFP and AID-tagged CAP-H2 gene, NCAPH2 disruption, random integration of X. laevis Cdk1, CDK1 disruption with HindIII
File
Contact List-replicate (pairs)
4DNFI8ALSRB8
204.64m
51.977%
21.243%
26.78%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNES6FARLK8
Multiple Experiments
File
Contact Matrix (mcool)
4DNFI4C9A3KH
None
Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEXBJKTWVH
Bio Rep 1, Tec Rep 1
Dilution Hi-C on DT40 with random integration of GFP and AID-tagged CAP-H2 gene, NCAPH2 disruption, random integration of X. laevis Cdk1, CDK1 disruption with HindIII
File
Alignments (bam)
4DNFICUNNHKL
112.18m
6.504%
12.678%
50.356%
0.008%
0.446%
Experiment
4DNEX61FZW4H
Bio Rep 2, Tec Rep 1
Dilution Hi-C on DT40 with random integration of GFP and AID-tagged CAP-H2 gene, NCAPH2 disruption, random integration of X. laevis Cdk1, CDK1 disruption with HindIII
File
Alignments (bam)
4DNFIF2I66Y9
387.59m
18.186%
10.376%
18.636%
0.003%
0.34%