ExperimentSetReplicate

ExperimentSet4DNESSU8NFVC
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dilution Hi-C on CAPH-mAID cells in prometaphase (60m post G2 block, nocodazole treated, CAPH-)

   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-H gene, random integration of X. laevis Cdk1, CDK1 disruption, random integration of CAP-H gene, CAP-H gene deletion
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
4DNESSU8NFVC
Multiple Experiments
File
Contact List-combined (pairs)
4DNFI9FQOK8L
393.55m
32.13%
23.859%
44.011%
Experiment
4DNEXDYG6GLB
Bio Rep 1, Tec Rep 1
Dilution Hi-C on DT40 with random integration of GFP and AID-tagged CAP-H gene, random integration of X. laevis Cdk1, CDK1 disruption, random integration of CAP-H gene, CAP-H gene deletion with HindIII
File
Contact List-replicate (pairs)
4DNFIGM2FX4X
185.97m
27.457%
24.478%
48.066%
Experiment
4DNEXLLAUZP9
Bio Rep 2, Tec Rep 1
Dilution Hi-C on DT40 with random integration of GFP and AID-tagged CAP-H gene, random integration of X. laevis Cdk1, CDK1 disruption, random integration of CAP-H gene, CAP-H gene deletion with HindIII
File
Contact List-replicate (pairs)
4DNFI2Q5RHQX
207.57m
36.316%
23.305%
40.379%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNESSU8NFVC
Multiple Experiments
File
Contact Matrix (mcool)
4DNFIDAP8JG2
None
Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEXDYG6GLB
Bio Rep 1, Tec Rep 1
Dilution Hi-C on DT40 with random integration of GFP and AID-tagged CAP-H gene, random integration of X. laevis Cdk1, CDK1 disruption, random integration of CAP-H gene, CAP-H gene deletion with HindIII
File
Alignments (bam)
4DNFIBCHYAMB
371.76m
16.175%
10.858%
22.939%
0.003%
0.393%
Experiment
4DNEXLLAUZP9
Bio Rep 2, Tec Rep 1
Dilution Hi-C on DT40 with random integration of GFP and AID-tagged CAP-H gene, random integration of X. laevis Cdk1, CDK1 disruption, random integration of CAP-H gene, CAP-H gene deletion with HindIII
File
Alignments (bam)
4DNFIHLEU96J
396.03m
15.937%
11.265%
20.38%
0.004%
0.439%