ExperimentSetReplicate

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ExperimentSet4DNESWX1J3QU
released
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Replicates of H3K4me3 PLAC-seq on K562 cells

   June 16th, 2021 at 7:01pm
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

Experiment Set Properties  

Set Type 
Replicate
Organism 
H. sapiens
Sample Type 
immortalized cells
Sample 
K562 (Tier 2)
Experiment Type(s) 
PLAC-seq
Modification Type 
None
Treatment Type 
None
Assay Details 
Target: H3K4me3

7 Processed Files

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Experiment
File
File Type
File Size
Notes
From Multiple Experiments
4DNESWX1J3QU
Multiple Experiments
File
4DNFI33H8F87
contact list-combined (pairs)
3.46 GB
-
File
4DNFIB52PNGQ
contact matrix (hic)
1.72 GB
-
File
4DNFINDGV53G
contact matrix (mcool)
1.07 GB
Experiment
4DNEXRI3VAH3
Bio Rep 1, Tec Rep 1
PLAC-seq against H3K4me3 on K562 (Tier 2)
File
4DNFIHRNTDUN
alignments (bam)
34.98 GB
-
File
4DNFIIU9FJYU
contact list-replicate (pairs)
1.9 GB
-
Experiment
4DNEX2S1FUHN
Bio Rep 2, Tec Rep 1
PLAC-seq against H3K4me3 on K562 (Tier 2)
File
4DNFIUBN447H
alignments (bam)
33.67 GB
-
File
4DNFIQGPB4PA
contact list-replicate (pairs)
1.86 GB
-

Quality Metrics

Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Details
From Multiple Experiments
4DNESWX1J3QU
Multiple Experiments
File
Contact List-combined (pairs)
4DNFI33H8F87
192.83m
58.372%
25.766%
15.862%
Experiment
4DNEXRI3VAH3
Bio Rep 1, Tec Rep 1
PLAC-seq against H3K4me3 on K562 (Tier 2)
File
Contact List-replicate (pairs)
4DNFIIU9FJYU
97.35m
58.154%
25.894%
15.952%
Experiment
4DNEX2S1FUHN
Bio Rep 2, Tec Rep 1
PLAC-seq against H3K4me3 on K562 (Tier 2)
File
Contact List-replicate (pairs)
4DNFIQGPB4PA
95.48m
58.594%
25.635%
15.77%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNESWX1J3QU
Multiple Experiments
File
Contact Matrix (mcool)
4DNFINDGV53G
1000; 2000; 5000; 10000; 25000; 50000; 100000; 250000; 500000; 1000000; 2500000; 5000000; 10000000
Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEXRI3VAH3
Bio Rep 1, Tec Rep 1
PLAC-seq against H3K4me3 on K562 (Tier 2)
File
Alignments (bam)
4DNFIHRNTDUN
158.45m
15.57%
12.414%
5.295%
5.286%
0.222%
Experiment
4DNEX2S1FUHN
Bio Rep 2, Tec Rep 1
PLAC-seq against H3K4me3 on K562 (Tier 2)
File
Alignments (bam)
4DNFIUBN447H
155.89m
14.837%
12.388%
6.097%
5.429%
0.223%