ExperimentSetReplicate

ExperimentSet4DNESH5M9J3U
released
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In situ Hi-C with HindIII on HeLa-S3 (mitotic) with 1% Formaldehyde and 3mM DSG 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
4DNESH5M9J3U
Multiple Experiments
File
Contact List-combined (pairs)
4DNFI2FTC51I
212.25m
69.632%
26.897%
3.471%
Experiment
4DNEXVH3GE23
Bio Rep 1, Tec Rep 1
in situ Hi-C on HeLa-S3 with HindIII
File
Contact List-replicate (pairs)
4DNFI2IP4RRY
212.25m
69.632%
26.897%
3.471%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNESH5M9J3U
Multiple Experiments
File
Contact Matrix (mcool)
4DNFICNP5H53
1000; 2000; 5000; 10000; 25000; 50000; 100000; 250000; 500000; 1000000
Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEXVH3GE23
Bio Rep 1, Tec Rep 1
in situ Hi-C on HeLa-S3 with HindIII
File
Alignments (bam)
4DNFIL5EFKNU
387.13m
11.738%
14.27%
19.162%
0.003%
0.072%