ExperimentSetReplicate

Browser Suggestion

Google Chrome  or Mozilla Firefox are the recommended browser(s) for using the 4DN Data Portal.

Microsoft Edge, Safari, Opera etc. should work for a majority of portal functions but are not explicitly supported and may present some glitches, e.g. during submission.

ExperimentSet4DNESNPYVXDM
released
View JSON

Replicates of in situ DNase Hi-C on CRISPR/cas9-modified Patski cells (Del-Dxz4)

   February 6th, 2018 at 9:57pm
Source Publication
Orientation-dependent Dxz4 contacts shape the 3D structure of the inactive X chromosome.
Bonora G, Deng X, et al., Nature communications 2018

Assay Description  

Experiment Set Properties  

Set Type 
Replicate
Organism 
M. musculus
Sample Type 
immortalized cells
Sample 
Patski
Experiment Type(s) 
DNase Hi-C
Modification Type 
Crispr
Treatment Type 
None
Assay Details 
Enzyme: DNaseI

8 Processed Files

    Explore Data

Loading
Experiment
File
File Type
File Size
Notes
From Multiple Experiments
4DNESNPYVXDM
Multiple Experiments
File
4DNFICAV2SHE
contact list-combined (pairs)
2.78 GB
-
File
4DNFIZXJ9ZEG
contact matrix (hic)
1.39 GB
-
File
4DNFIT8EVQOK
contact matrix (mcool)
1.34 GB
File
4DNFI24IU8J1
compartments (bw)
186.48 kB
-
File
4DNFIIP1UOJ7
boundaries (bed)
205.15 kB
-
File
4DNFISSCK8BH
insulation score-diamond (bw)
6.93 MB
-
Experiment
4DNEXBH5B94I
Bio Rep 1, Tec Rep 1
DNase Hi-C on Patski with DNaseI
File
4DNFI5U8RMQT
alignments (bam)
144.8 GB
-
File
4DNFIEJIO7TQ
contact list-replicate (pairs)
2.78 GB
-

Quality Metrics

Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Details
From Multiple Experiments
4DNESNPYVXDM
Multiple Experiments
File
Contact List-combined (pairs)
4DNFICAV2SHE
148.27m
25.738%
53.046%
21.216%
Experiment
4DNEXBH5B94I
Bio Rep 1, Tec Rep 1
DNase Hi-C on Patski with DNaseI
File
Contact List-replicate (pairs)
4DNFIEJIO7TQ
148.27m
25.738%
53.046%
21.216%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNESNPYVXDM
Multiple Experiments
File
Contact Matrix (mcool)
4DNFIT8EVQOK
None
Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEXBH5B94I
Bio Rep 1, Tec Rep 1
DNase Hi-C on Patski with DNaseI
File
Alignments (bam)
4DNFI5U8RMQT
502.61m
10.232%
16.891%
9.585%
33.792%
0.062%