ExperimentSetReplicate

ExperimentSet4DNES25ABNZ1
released
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in situ Hi-C on 24 hour activated B cells, treated with oligomycin (2 hour) to deplete ATP

   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

26 Processed Files

Quality Metrics

Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Report
Details
From Multiple Experiments
4DNES25ABNZ1
Multiple Experiments
File
Contact List-combined (pairs)
4DNFIZDZQTIA
1.87 billion
58.597%
15.093%
26.309%
Experiment
4DNEXJOPJ4E5
Bio Rep 1, Tec Rep 1
in situ Hi-C on B cell derived cell line with MboI
File
Contact List-replicate (pairs)
4DNFIQE5RLII
182.36m
56.765%
12.189%
31.046%
Experiment
4DNEX7RMOD2M
Bio Rep 2, Tec Rep 1
in situ Hi-C on B cell derived cell line with MboI
File
Contact List-replicate (pairs)
4DNFICJ9EQCJ
348.76m
57.732%
12.237%
30.031%
Experiment
4DNEXS729LEL
Bio Rep 3, Tec Rep 1
in situ Hi-C on B cell derived cell line with MboI
File
Contact List-replicate (pairs)
4DNFIGBSZ341
254.88m
59.314%
12.455%
28.23%
Experiment
4DNEX9VSC6VO
Bio Rep 4, Tec Rep 1
in situ Hi-C on B cell derived cell line with MboI
File
Contact List-replicate (pairs)
4DNFI5EX5MRJ
100.67m
54.933%
13.775%
31.292%
Experiment
4DNEXKVS2H27
Bio Rep 5, Tec Rep 1
in situ Hi-C on B cell derived cell line with MboI
File
Contact List-replicate (pairs)
4DNFIB6B1U2D
149.54m
58.773%
17.068%
24.16%
Experiment
4DNEXXJ3QQ26
Bio Rep 6, Tec Rep 1
in situ Hi-C on B cell derived cell line with MboI
File
Contact List-replicate (pairs)
4DNFID63HED4
122.03m
60.643%
15.683%
23.673%
Experiment
4DNEXFYVHS7F
Bio Rep 7, Tec Rep 1
in situ Hi-C on B cell derived cell line with MboI
File
Contact List-replicate (pairs)
4DNFISF8KCG1
184.73m
58.923%
17.471%
23.606%
Experiment
4DNEXYCAAWT1
Bio Rep 8, Tec Rep 1
in situ Hi-C on B cell derived cell line with MboI
File
Contact List-replicate (pairs)
4DNFI4ASDIZO
400.61m
59.148%
18.354%
22.498%
Experiment
4DNEX9Q6SQZC
Bio Rep 9, Tec Rep 1
in situ Hi-C on B cell derived cell line with MboI
File
Contact List-replicate (pairs)
4DNFIPW6E5VY
74.25m
60.458%
17.29%
22.252%
Experiment
4DNEXD85865V
Bio Rep 10, Tec Rep 1
in situ Hi-C on B cell derived cell line with MboI
File
Contact List-replicate (pairs)
4DNFIDVI9LH2
51.92m
61.052%
16.154%
22.794%
Show 4 More
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNES25ABNZ1
Multiple Experiments
File
Contact Matrix (mcool)
4DNFIAVHP5AV
None
Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEXJOPJ4E5
Bio Rep 1, Tec Rep 1
in situ Hi-C on B cell derived cell line with MboI
File
Alignments (bam)
4DNFIFGRRUL2
272.82m
7.844%
11.666%
4.222%
9.426%
0.155%
Experiment
4DNEX7RMOD2M
Bio Rep 2, Tec Rep 1
in situ Hi-C on B cell derived cell line with MboI
File
Alignments (bam)
4DNFIAKY77NS
529.78m
9.789%
11.33%
4.128%
8.923%
0.146%
Experiment
4DNEXS729LEL
Bio Rep 3, Tec Rep 1
in situ Hi-C on B cell derived cell line with MboI
File
Alignments (bam)
4DNFI7EAO3LY
381.11m
7.883%
11.476%
4.627%
9.136%
0.143%
Experiment
4DNEX9VSC6VO
Bio Rep 4, Tec Rep 1
in situ Hi-C on B cell derived cell line with MboI
File
Alignments (bam)
4DNFIC4C9M8Q
158.97m
10.29%
11.646%
4.948%
9.79%
0.153%
Experiment
4DNEXKVS2H27
Bio Rep 5, Tec Rep 1
in situ Hi-C on B cell derived cell line with MboI
File
Alignments (bam)
4DNFIA134ZJZ
222.09m
7.292%
12.341%
4.347%
8.687%
0.138%
Experiment
4DNEXXJ3QQ26
Bio Rep 6, Tec Rep 1
in situ Hi-C on B cell derived cell line with MboI
File
Alignments (bam)
4DNFIQODQMAM
180.37m
6.822%
12.164%
4.591%
8.769%
0.132%
Experiment
4DNEXFYVHS7F
Bio Rep 7, Tec Rep 1
in situ Hi-C on B cell derived cell line with MboI
File
Alignments (bam)
4DNFIK2LXT9H
289.06m
9.2%
11.97%
5.797%
9.125%
0.123%
Experiment
4DNEXYCAAWT1
Bio Rep 8, Tec Rep 1
in situ Hi-C on B cell derived cell line with MboI
File
Alignments (bam)
4DNFI86XY4W3
605.75m
6.383%
12.218%
6.126%
9.139%
0.118%
Experiment
4DNEX9Q6SQZC
Bio Rep 9, Tec Rep 1
in situ Hi-C on B cell derived cell line with MboI
File
Alignments (bam)
4DNFINIP2PA1
110.17m
6.937%
12.182%
4.743%
8.738%
0.128%
Experiment
4DNEXD85865V
Bio Rep 10, Tec Rep 1
in situ Hi-C on B cell derived cell line with MboI
File
Alignments (bam)
4DNFIOMK2RVN
75.76m
7.173%
11.877%
3.946%
8.478%
0.128%