ExperimentSetReplicate

ExperimentSet4DNESE1VMAMD
released
View JSON

in situ Hi-C on 30 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

18 Processed Files

Quality Metrics

Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Report
Details
From Multiple Experiments
4DNESE1VMAMD
Multiple Experiments
File
Contact List-combined (pairs)
4DNFI27I3P1V
383.78m
58.546%
26.408%
15.047%
Experiment
4DNEXW8BROD1
Bio Rep 1, Tec Rep 1
in situ Hi-C on B cell derived cell line with MboI
File
Contact List-replicate (pairs)
4DNFIW658YW8
61.52m
55.631%
30.04%
14.329%
Experiment
4DNEX4117Y6M
Bio Rep 2, Tec Rep 1
in situ Hi-C on B cell derived cell line with MboI
File
Contact List-replicate (pairs)
4DNFIIS2LVM6
70.26m
60.037%
24.55%
15.413%
Experiment
4DNEXB4BMJKZ
Bio Rep 3, Tec Rep 1
in situ Hi-C on B cell derived cell line with MboI
File
Contact List-replicate (pairs)
4DNFICCMF8VA
49.38m
60.027%
24.774%
15.199%
Experiment
4DNEX8B6PEVL
Bio Rep 4, Tec Rep 1
in situ Hi-C on B cell derived cell line with MboI
File
Contact List-replicate (pairs)
4DNFI1FWENNA
66.76m
54.6%
31.547%
13.853%
Experiment
4DNEX4QJ4ZLB
Bio Rep 5, Tec Rep 1
in situ Hi-C on B cell derived cell line with MboI
File
Contact List-replicate (pairs)
4DNFIBE4QMQI
67.93m
60.809%
23.751%
15.44%
Experiment
4DNEXV485ZVS
Bio Rep 6, Tec Rep 1
in situ Hi-C on B cell derived cell line with MboI
File
Contact List-replicate (pairs)
4DNFI685MLL2
67.93m
60.181%
23.832%
15.987%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNESE1VMAMD
Multiple Experiments
File
Contact Matrix (mcool)
4DNFISA93XFU
None
Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEXW8BROD1
Bio Rep 1, Tec Rep 1
in situ Hi-C on B cell derived cell line with MboI
File
Alignments (bam)
4DNFIIODRJGM
87.29m
7.313%
15.928%
1.963%
4.321%
0.146%
Experiment
4DNEX4117Y6M
Bio Rep 2, Tec Rep 1
in situ Hi-C on B cell derived cell line with MboI
File
Alignments (bam)
4DNFI8U3Z6PW
99.57m
7.369%
16.003%
1.58%
4.48%
0.083%
Experiment
4DNEXB4BMJKZ
Bio Rep 3, Tec Rep 1
in situ Hi-C on B cell derived cell line with MboI
File
Alignments (bam)
4DNFI874TJYJ
70.28m
7.634%
16.231%
1.559%
4.322%
0.096%
Experiment
4DNEX8B6PEVL
Bio Rep 4, Tec Rep 1
in situ Hi-C on B cell derived cell line with MboI
File
Alignments (bam)
4DNFIV5V65X9
94.76m
7.652%
15.085%
1.91%
4.903%
0.152%
Experiment
4DNEX4QJ4ZLB
Bio Rep 5, Tec Rep 1
in situ Hi-C on B cell derived cell line with MboI
File
Alignments (bam)
4DNFIZYZNEN7
96.37m
7.446%
16.108%
1.467%
4.491%
0.094%
Experiment
4DNEXV485ZVS
Bio Rep 6, Tec Rep 1
in situ Hi-C on B cell derived cell line with MboI
File
Alignments (bam)
4DNFIUGHWBEE
97.34m
8.05%
16.14%
1.609%
4.421%
0.091%