ExperimentSetReplicate

ExperimentSet4DNES2253IBO
released
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in situ Hi-C on human embryonic stem cells (H1) treated with ammonium acetate - NH4OAc

   July 1st, 2021 at 5:48pm
Source Publication
Genome-wide analysis of the interplay between chromatin-associated RNA and 3D genome organization in human cells.
Calandrelli R, Wen X, et al., Nature communications 2023

Assay Description  

Experiment Set Properties  

Set Type 
Replicate
Organism 
H. sapiens
Sample Type 
stem cells
Sample 
H1-hESC (Tier 1)
Experiment Type(s) 
in situ Hi-C
Modification Type 
None
Treatment Type 
Chemical
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
4DNES2253IBO
Multiple Experiments
File
Contact List-combined (pairs)
4DNFIWC5NBEC
418.3m
55.092%
22.338%
22.57%
Experiment
4DNEXT7PZCJM
Bio Rep 1, Tec Rep 1
in situ Hi-C on H1-hESC (Tier 1) with Arima - A1, A2
File
Contact List-replicate (pairs)
4DNFIL8E39EJ
202.68m
53.716%
24.001%
22.283%
Experiment
4DNEXVT4AUEP
Bio Rep 2, Tec Rep 1
in situ Hi-C on H1-hESC (Tier 1) with Arima - A1, A2
File
Contact List-replicate (pairs)
4DNFIQQ83MLI
215.62m
56.384%
20.775%
22.84%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNES2253IBO
Multiple Experiments
File
Contact Matrix (mcool)
4DNFIJ2XM4JW
None
Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEXT7PZCJM
Bio Rep 1, Tec Rep 1
in situ Hi-C on H1-hESC (Tier 1) with Arima - A1, A2
File
Alignments (bam)
4DNFIR5MJCBM
310.31m
9.024%
11.464%
3.91%
10.288%
0.221%
Experiment
4DNEXVT4AUEP
Bio Rep 2, Tec Rep 1
in situ Hi-C on H1-hESC (Tier 1) with Arima - A1, A2
File
Alignments (bam)
4DNFIJGJSV13
302.79m
8.219%
10.612%
1.421%
8.538%
0.192%