ExperimentSetReplicate

ExperimentSet4DNES3O1B45O
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in situ Hi-C on 30 hour activated B cells, treated with hydroxyurea to inhibit DNA replication

   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

18 Processed Files

Quality Metrics

Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Report
Details
From Multiple Experiments
4DNES3O1B45O
Multiple Experiments
File
Contact List-combined (pairs)
4DNFICWOYIG9
339.74m
50.792%
24.812%
24.396%
Experiment
4DNEX4JMQO9U
Bio Rep 1, Tec Rep 1
in situ Hi-C on B cell derived cell line with MboI
File
Contact List-replicate (pairs)
4DNFI9UF7F9T
53.43m
49.306%
27.906%
22.788%
Experiment
4DNEXVKRYYDB
Bio Rep 2, Tec Rep 1
in situ Hi-C on B cell derived cell line with MboI
File
Contact List-replicate (pairs)
4DNFI6EYQZDY
59.35m
51.085%
23.968%
24.947%
Experiment
4DNEXKS17DNT
Bio Rep 3, Tec Rep 1
in situ Hi-C on B cell derived cell line with MboI
File
Contact List-replicate (pairs)
4DNFI7NXIRH6
59.55m
51.21%
23.724%
25.065%
Experiment
4DNEXBAR7DBY
Bio Rep 4, Tec Rep 1
in situ Hi-C on B cell derived cell line with MboI
File
Contact List-replicate (pairs)
4DNFIGDCYUUI
48.41m
49.384%
27.368%
23.248%
Experiment
4DNEX4Y655YT
Bio Rep 5, Tec Rep 1
in situ Hi-C on B cell derived cell line with MboI
File
Contact List-replicate (pairs)
4DNFI8GNBO44
60.48m
51.872%
23.43%
24.698%
Experiment
4DNEXFPMBMV8
Bio Rep 6, Tec Rep 1
in situ Hi-C on B cell derived cell line with MboI
File
Contact List-replicate (pairs)
4DNFI223CD1L
58.53m
51.476%
23.261%
25.262%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNES3O1B45O
Multiple Experiments
File
Contact Matrix (mcool)
4DNFIRUZBSGM
None
Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEX4JMQO9U
Bio Rep 1, Tec Rep 1
in situ Hi-C on B cell derived cell line with MboI
File
Alignments (bam)
4DNFIOACVNNS
77.39m
7.525%
17.202%
2.099%
4.143%
0.093%
Experiment
4DNEXVKRYYDB
Bio Rep 2, Tec Rep 1
in situ Hi-C on B cell derived cell line with MboI
File
Alignments (bam)
4DNFI7JOH4P6
87.58m
7.784%
18.5%
1.762%
4.186%
0.09%
Experiment
4DNEXKS17DNT
Bio Rep 3, Tec Rep 1
in situ Hi-C on B cell derived cell line with MboI
File
Alignments (bam)
4DNFIIBQWS83
87.83m
8.707%
17.443%
1.499%
4.554%
0.092%
Experiment
4DNEXBAR7DBY
Bio Rep 4, Tec Rep 1
in situ Hi-C on B cell derived cell line with MboI
File
Alignments (bam)
4DNFIO3M7EQN
69.94m
7.654%
16.806%
2.1%
4.216%
0.089%
Experiment
4DNEX4Y655YT
Bio Rep 5, Tec Rep 1
in situ Hi-C on B cell derived cell line with MboI
File
Alignments (bam)
4DNFI9SVFUMS
88.62m
7.674%
18.101%
1.731%
4.251%
0.089%
Experiment
4DNEXFPMBMV8
Bio Rep 6, Tec Rep 1
in situ Hi-C on B cell derived cell line with MboI
File
Alignments (bam)
4DNFIGKE9VGX
85.19m
7.551%
17.473%
1.662%
4.613%
0.092%