ExperimentSetReplicate

ExperimentSet4DNES1QUXG92
released
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Replicates of F123 CAST X 129 mouse cells containing a genomically modified AID-tagged CTCF treated with Auxin for 96 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
4DNES1QUXG92
Multiple Experiments
File
Contact List-combined (pairs)
4DNFIW3YHQXS
452.92m
27.914%
58.204%
13.882%
Experiment
4DNEXRI9JYW6
Bio Rep 1, Tec Rep 1
in situ Hi-C on F123-CASTx129 (Tier 2) with MboI
File
Contact List-replicate (pairs)
4DNFI6S3I9XZ
326.15m
34.673%
48.75%
16.577%
Experiment
4DNEX4J4Z9WE
Bio Rep 2, Tec Rep 1
in situ Hi-C on F123-CASTx129 (Tier 2) with MboI
File
Contact List-replicate (pairs)
4DNFIUZJOJW9
126.77m
10.527%
82.524%
6.95%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNES1QUXG92
Multiple Experiments
File
Contact Matrix (mcool)
4DNFI7Z381GX
None
Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEXRI9JYW6
Bio Rep 1, Tec Rep 1
in situ Hi-C on F123-CASTx129 (Tier 2) with MboI
File
Alignments (bam)
4DNFI12DLPLR
639.35m
9.895%
27.799%
11.221%
0.072%
0.106%
Experiment
4DNEX4J4Z9WE
Bio Rep 2, Tec Rep 1
in situ Hi-C on F123-CASTx129 (Tier 2) with MboI
File
Alignments (bam)
4DNFI5TVC4OY
256.36m
9.353%
34.799%
6.335%
0.063%
0.146%