ExperimentSetReplicate

ExperimentSet4DNESZGE3UM2
released
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In situ Hi-C with HindIII on HeLa-S3 (mitotic) with 1% Formaldehyde and 3mM EGS crosslinking

   June 27th, 2020 at 6:56pm
Source Publication
Systematic evaluation of chromosome conformation capture assays.
Akgol Oksuz B, Yang L, et al., Nature methods 2021

Assay Description  

Experiment Set Properties  

Set Type 
Replicate
Organism 
H. sapiens
Sample Type 
immortalized cells
Sample 
HeLa-S3
Experiment Type(s) 
in situ Hi-C
Modification Type 
None
Treatment Type 
Chemical
Assay Details 
Enzyme: HindIII

5 Processed Files

Quality Metrics

Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Report
Details
From Multiple Experiments
4DNESZGE3UM2
Multiple Experiments
File
Contact List-combined (pairs)
4DNFIO8CHKOI
210.08m
72.475%
22.5%
5.026%
Experiment
4DNEX286UZDL
Bio Rep 1, Tec Rep 1
in situ Hi-C on HeLa-S3 with HindIII
File
Contact List-replicate (pairs)
4DNFIXJOFD63
210.08m
72.475%
22.5%
5.026%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNESZGE3UM2
Multiple Experiments
File
Contact Matrix (mcool)
4DNFI2SNB5Z9
1000; 2000; 5000; 10000; 25000; 50000; 100000; 250000; 500000
Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEX286UZDL
Bio Rep 1, Tec Rep 1
in situ Hi-C on HeLa-S3 with HindIII
File
Alignments (bam)
4DNFIJKBWBI2
388.32m
12.173%
14.332%
19.392%
0.003%
0.082%