ExperimentSetReplicate

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ExperimentSet4DNESIKCVASO
released
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iMARGI on chronic myelogenous leukemia lymphoblasts (K562)

   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 
immortalized cells
Sample 
K562 (Tier 2)
Experiment Type(s) 
MARGI
Modification Type 
None
Treatment Type 
None
Assay Details 
Enzyme: AluI

10 Processed Files

    Explore Data

Loading
Experiment
File
File Type
File Size
Notes
From Multiple Experiments
4DNESIKCVASO
Multiple Experiments
File
4DNFIVIHUHOE
contact list-combined (pairs)
6.84 GB
-
File
4DNFIOHY9ZX7
contact matrix (mcool)
1.9 GB
Experiment
4DNEXMAFL7MZ
Bio Rep 1, Tec Rep 1
MARGI on K562 (Tier 2)
File
4DNFI5V3QPM1
alignments (bam)
63.78 GB
-
File
4DNFI9SZVQU5
contact list-replicate (pairs)
1.95 GB
-
File
4DNFIKDM6PEK
alignments (bam)
65.17 GB
-
File
4DNFIOE1EASE
contact list-replicate (pairs)
2.05 GB
-
Experiment
4DNEXFDN2NC9
Bio Rep 2, Tec Rep 1
MARGI on K562 (Tier 2)
File
4DNFIVW3RNTH
alignments (bam)
67.95 GB
-
File
4DNFIG1V7TCM
contact list-replicate (pairs)
2.21 GB
-
File
4DNFIHY3RY4H
alignments (bam)
67.45 GB
-
File
4DNFISX1N9YZ
contact list-replicate (pairs)
2.22 GB
-

Quality Metrics

Experiment
For File
Filtered Reads
Cis reads (>200000)
Short cis reads
Trans Reads
Details
From Multiple Experiments
4DNESIKCVASO
Multiple Experiments
File
Contact List-combined (pairs)
4DNFIVIHUHOE
248.41m
16.609%
22.61%
60.781%
Experiment
4DNEXMAFL7MZ
Bio Rep 1, Tec Rep 1
MARGI on K562 (Tier 2)
File
Contact List-replicate (pairs)
4DNFI9SZVQU5
57.25m
16.452%
23.558%
59.99%
File
Contact List-replicate (pairs)
4DNFIOE1EASE
60.37m
16.482%
23.495%
60.023%
Experiment
4DNEXFDN2NC9
Bio Rep 2, Tec Rep 1
MARGI on K562 (Tier 2)
File
Contact List-replicate (pairs)
4DNFIG1V7TCM
65.3m
16.722%
21.827%
61.451%
File
Contact List-replicate (pairs)
4DNFISX1N9YZ
65.5m
16.75%
21.748%
61.503%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNESIKCVASO
Multiple Experiments
File
Contact Matrix (mcool)
4DNFIOHY9ZX7
1000; 2000; 5000; 10000; 25000; 50000; 100000; 250000; 500000; 1000000; 2500000; 5000000; 10000000