ExperimentSetReplicate

ExperimentSet4DNESYX7AQRY
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in situ Hi-C on 24 hour activated B cells

   November 27th, 2018 at 6:26pm
Source Publication
The Energetics and Physiological Impact of Cohesin Extrusion.
Vian L, Pekowska A, et al., Cell 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 
M. musculus
Sample Type 
primary cells
Sample 
B cell derived cell line
Experiment Type(s) 
in situ Hi-C
Modification Type 
None
Treatment Type 
Chemical
Assay Details 
Enzyme: MboI

22 Processed Files

Quality Metrics

Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Report
Details
From Multiple Experiments
4DNESYX7AQRY
Multiple Experiments
File
Contact List-combined (pairs)
4DNFIFBBAKK4
1.13 billion
54.75%
21.875%
23.376%
Experiment
4DNEX3JZD5GE
Bio Rep 1, Tec Rep 1
in situ Hi-C on B cell derived cell line with MboI
File
Contact List-replicate (pairs)
4DNFIJ9MX4TG
102.31m
53.348%
25.043%
21.609%
Experiment
4DNEX7RGB2RO
Bio Rep 2, Tec Rep 1
in situ Hi-C on B cell derived cell line with MboI
File
Contact List-replicate (pairs)
4DNFIU16CPPI
200.8m
54.96%
21.606%
23.434%
Experiment
4DNEXGJ6R1Y4
Bio Rep 3, Tec Rep 1
in situ Hi-C on B cell derived cell line with MboI
File
Contact List-replicate (pairs)
4DNFI46QCLON
44.97m
52.499%
25.343%
22.158%
Experiment
4DNEXGFN4TGR
Bio Rep 4, Tec Rep 1
in situ Hi-C on B cell derived cell line with MboI
File
Contact List-replicate (pairs)
4DNFIT23KY5M
47.7m
52.598%
24.796%
22.605%
Experiment
4DNEXN6K8PVG
Bio Rep 5, Tec Rep 1
in situ Hi-C on B cell derived cell line with MboI
File
Contact List-replicate (pairs)
4DNFIRV6PZMQ
362.11m
55.118%
20.304%
24.578%
Experiment
4DNEXH7GPUTR
Bio Rep 6, Tec Rep 1
in situ Hi-C on B cell derived cell line with MboI
File
Contact List-replicate (pairs)
4DNFI5J9O8P3
203.02m
54.678%
20.467%
24.855%
Experiment
4DNEXH55ZQCC
Bio Rep 7, Tec Rep 1
in situ Hi-C on B cell derived cell line with MboI
File
Contact List-replicate (pairs)
4DNFIHIASISO
80.81m
55.627%
22.378%
21.995%
Experiment
4DNEXP5PSDTH
Bio Rep 8, Tec Rep 1
in situ Hi-C on B cell derived cell line with MboI
File
Contact List-replicate (pairs)
4DNFITF9B9GL
83.57m
56.129%
24.847%
19.024%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNESYX7AQRY
Multiple Experiments
File
Contact Matrix (mcool)
4DNFIPNP9H9T
None
Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEX3JZD5GE
Bio Rep 1, Tec Rep 1
in situ Hi-C on B cell derived cell line with MboI
File
Alignments (bam)
4DNFI5NRKYDJ
146.8m
6.053%
16.4%
3.824%
4.026%
0.127%
Experiment
4DNEX7RGB2RO
Bio Rep 2, Tec Rep 1
in situ Hi-C on B cell derived cell line with MboI
File
Alignments (bam)
4DNFIVQFAOAK
286.42m
7.022%
17.504%
1.966%
3.404%
0.124%
Experiment
4DNEXGJ6R1Y4
Bio Rep 3, Tec Rep 1
in situ Hi-C on B cell derived cell line with MboI
File
Alignments (bam)
4DNFIHUR9I5K
64.21m
6.52%
18.348%
1.75%
3.338%
0.137%
Experiment
4DNEXGFN4TGR
Bio Rep 4, Tec Rep 1
in situ Hi-C on B cell derived cell line with MboI
File
Alignments (bam)
4DNFIUU6W1VP
68.08m
6.56%
18.29%
1.769%
3.325%
0.128%
Experiment
4DNEXN6K8PVG
Bio Rep 5, Tec Rep 1
in situ Hi-C on B cell derived cell line with MboI
File
Alignments (bam)
4DNFI7KICUTA
520.48m
6.88%
17.179%
2.609%
3.759%
0.121%
Experiment
4DNEXH7GPUTR
Bio Rep 6, Tec Rep 1
in situ Hi-C on B cell derived cell line with MboI
File
Alignments (bam)
4DNFIY4UR6CV
290.5m
6.875%
17.658%
1.953%
3.626%
0.124%
Experiment
4DNEXH55ZQCC
Bio Rep 7, Tec Rep 1
in situ Hi-C on B cell derived cell line with MboI
File
Alignments (bam)
4DNFIFX81N88
117.01m
7.717%
17.875%
1.558%
3.789%
0.115%
Experiment
4DNEXP5PSDTH
Bio Rep 8, Tec Rep 1
in situ Hi-C on B cell derived cell line with MboI
File
Alignments (bam)
4DNFIU7HIVVU
120.54m
7.415%
17.82%
1.815%
3.623%
0.119%