ExperimentSetReplicate

ExperimentSet4DNESQMM4EBN
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Replicates of F123 CAST X 129 mouse cells containing a genomically modified AID-tagged CTCF treated with Auxin for 24 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
4DNESQMM4EBN
Multiple Experiments
File
Contact List-combined (pairs)
4DNFI6TWSN91
411.2m
33.463%
56.604%
9.933%
Experiment
4DNEXLWC9JX7
Bio Rep 1, Tec Rep 1
in situ Hi-C on F123-CASTx129 (Tier 2) with MboI
File
Contact List-replicate (pairs)
4DNFIGU2ZYNE
261.95m
17.615%
73.005%
9.38%
Experiment
4DNEXU87YSSY
Bio Rep 2, Tec Rep 1
in situ Hi-C on F123-CASTx129 (Tier 2) with MboI
File
Contact List-replicate (pairs)
4DNFIVPADLI2
149.26m
61.277%
27.82%
10.903%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNESQMM4EBN
Multiple Experiments
File
Contact Matrix (mcool)
4DNFI2KWDAL6
None
Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEXLWC9JX7
Bio Rep 1, Tec Rep 1
in situ Hi-C on F123-CASTx129 (Tier 2) with MboI
File
Alignments (bam)
4DNFIRE2S3XE
646.15m
8.94%
30.526%
19.932%
0.062%
0.102%
Experiment
4DNEXU87YSSY
Bio Rep 2, Tec Rep 1
in situ Hi-C on F123-CASTx129 (Tier 2) with MboI
File
Alignments (bam)
4DNFIQIQHM8G
261.67m
11.98%
25.776%
5.129%
0.075%
0.086%