ExperimentSetReplicate

ExperimentSet4DNESYIMR82X
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dilution Hi-C on CAPH2-mAID cells in G2 (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
4DNESYIMR82X
Multiple Experiments
File
Contact List-combined (pairs)
4DNFI939ZHC5
324.97m
36.84%
45.276%
17.884%
Experiment
4DNEXMOSRYT5
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)
4DNFIWNT3P3U
126.26m
11.379%
83.169%
5.452%
Experiment
4DNEXOE3CU5G
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)
4DNFIAPPYPED
198.71m
53.017%
21.199%
25.784%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNESYIMR82X
Multiple Experiments
File
Contact Matrix (mcool)
4DNFI75T6RF1
None
Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEXMOSRYT5
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)
4DNFINMA6UXS
338.07m
9.52%
9.924%
43.203%
0.006%
0.317%
Experiment
4DNEXOE3CU5G
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)
4DNFIQRLYDAS
384.91m
18.813%
9.829%
19.73%
0.003%
0.302%