ExperimentSetReplicate

ExperimentSet4DNES1TMKQAN
released
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in situ Hi-C on TCF1 KO Scid.adh cell line

   October 18th, 2022 at 3:56pm
Source Publication
TCF-1 promotes chromatin interactions across topologically associating domains in T cell progenitors.
Wang W, Chandra A, et al., Nature immunology 2022

Assay Description  

Experiment Set Properties  

Set Type 
Replicate
Organism 
M. musculus
Sample Type 
immortalized cells
Sample 
scid.adh
Experiment Type(s) 
in situ Hi-C
Modification Type 
Crispr
Treatment Type 
None
Assay Details 
Enzyme: Arima - A1, A2

10 Processed Files

Quality Metrics

Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Report
Details
From Multiple Experiments
4DNES1TMKQAN
Multiple Experiments
File
Contact List-combined (pairs)
4DNFI3W7M5AB
1.02 billion
60.392%
29.981%
9.628%
Experiment
4DNEXK1LDDDU
Bio Rep 1, Tec Rep 1
in situ Hi-C on scid.adh with Arima - A1, A2
File
Contact List-replicate (pairs)
4DNFIM1QKY24
707.14m
58.887%
31.714%
9.398%
Experiment
4DNEXUYDF7OO
Bio Rep 2, Tec Rep 1
in situ Hi-C on scid.adh with Arima - A1, A2
File
Contact List-replicate (pairs)
4DNFI13MOCR1
316.18m
63.756%
26.104%
10.141%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNES1TMKQAN
Multiple Experiments
File
Contact Matrix (mcool)
4DNFIKHGZ22V
None
Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEXK1LDDDU
Bio Rep 1, Tec Rep 1
in situ Hi-C on scid.adh with Arima - A1, A2
File
Alignments (bam)
4DNFINZRWPSS
1.19 billion
12.529%
17.612%
7.366%
3.247%
0.071%
Experiment
4DNEXUYDF7OO
Bio Rep 2, Tec Rep 1
in situ Hi-C on scid.adh with Arima - A1, A2
File
Alignments (bam)
4DNFIPD5YQGB
515.01m
14.297%
21.838%
2.472%
0.0%
0.059%