ExperimentSetReplicate

ExperimentSet4DNESWDLDMGN
released
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Replicates of F123 CAST X 129 mouse cells containing a genomically modified AID-tagged CTCF treated with Auxin for 48 hours and then prepared for in situ Hi-C

   May 27th, 2018 at 4:58am
Source Publication
Promoter-proximal CTCF binding promotes distal enhancer-dependent gene activation.
Kubo N, Ishii H, et al., Nature structural & molecular biology 2021

Assay Description  

Experiment Set Properties  

Set Type 
Replicate
Organism 
M. musculus
Sample Type 
stem cells
Sample 
F123-CASTx129 (Tier 2)
Experiment Type(s) 
in situ Hi-C
Modification Type 
  1. Crispr
  2. Stable Transfection
Treatment Type 
Chemical
Assay Details 
Enzyme: MboI

10 Processed Files

Quality Metrics

Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Report
Details
From Multiple Experiments
4DNESWDLDMGN
Multiple Experiments
File
Contact List-combined (pairs)
4DNFIDHNCVEM
514.1m
52.181%
33.023%
14.796%
Experiment
4DNEXVGS8FQQ
Bio Rep 1, Tec Rep 1
in situ Hi-C on F123-CASTx129 (Tier 2) with MboI
File
Contact List-replicate (pairs)
4DNFIKYF3V7I
276.67m
45.701%
39.109%
15.19%
Experiment
4DNEXA7ZMMK3
Bio Rep 2, Tec Rep 1
in situ Hi-C on F123-CASTx129 (Tier 2) with MboI
File
Contact List-replicate (pairs)
4DNFIVMRIR5H
237.43m
59.732%
25.932%
14.337%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNESWDLDMGN
Multiple Experiments
File
Contact Matrix (mcool)
4DNFIC453HVL
None
Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEXVGS8FQQ
Bio Rep 1, Tec Rep 1
in situ Hi-C on F123-CASTx129 (Tier 2) with MboI
File
Alignments (bam)
4DNFITTS8G64
630.35m
10.93%
26.404%
18.698%
0.076%
0.085%
Experiment
4DNEXA7ZMMK3
Bio Rep 2, Tec Rep 1
in situ Hi-C on F123-CASTx129 (Tier 2) with MboI
File
Alignments (bam)
4DNFIPW15OGS
392.98m
10.919%
24.148%
4.438%
0.077%
0.086%