ExperimentSetReplicate

ExperimentSet4DNESD2QXAG5
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In situ Hi-C with DdeI on HFF cells 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 
HFF-hTERT
Experiment Type(s) 
in situ Hi-C
Modification Type 
None
Treatment Type 
None
Assay Details 
Enzyme: DdeI

8 Processed Files

Quality Metrics

Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Report
Details
From Multiple Experiments
4DNESD2QXAG5
Multiple Experiments
File
Contact List-combined (pairs)
4DNFIDZMDDXL
205.04m
44.099%
28.161%
27.74%
Experiment
4DNEXFU1OR7Q
Bio Rep 1, Tec Rep 1
in situ Hi-C on HFF-hTERT with DdeI
File
Contact List-replicate (pairs)
4DNFI3BLRSYT
205.04m
44.099%
28.161%
27.74%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNESD2QXAG5
Multiple Experiments
File
Contact Matrix (mcool)
4DNFIYELASMX
None
Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEXFU1OR7Q
Bio Rep 1, Tec Rep 1
in situ Hi-C on HFF-hTERT with DdeI
File
Alignments (bam)
4DNFIR6T9GTF
377.51m
14.431%
18.368%
12.882%
0.004%
0.113%