ExperimentSetReplicate

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ExperimentSet4DNES2NY639B
released
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Replicates of H3K4me3 PLAC-seq on Sox2 tagged F123 ES cells

   August 13th, 2020 at 6:05pm
Source Publication
CTCF mediates dosage- and sequence-context-dependent transcriptional insulation by forming local chromatin domains.
Huang H, Zhu Q, et al., Nature genetics 2021

Experiment Set Properties  

Set Type 
Replicate
Organism 
M. musculus
Sample Type 
stem cells
Sample 
F123-CASTx129 with Sox2 tags
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
4DNES2NY639B
Multiple Experiments
File
4DNFIQVG8HXI
contact list-combined (pairs)
2.06 GB
-
File
4DNFID4L8WZS
contact matrix (hic)
906.35 MB
-
File
4DNFIEJ4ED21
contact matrix (mcool)
559.15 MB
Experiment
4DNEX9IAX7HP
Bio Rep 1, Tec Rep 1
PLAC-seq against H3K4me3 on F123-CASTx129 with Sox2 tags
File
4DNFITUJU2KV
alignments (bam)
11.92 GB
-
File
4DNFICXRNO3Z
contact list-replicate (pairs)
1.01 GB
-
Experiment
4DNEXX456QN1
Bio Rep 2, Tec Rep 1
PLAC-seq against H3K4me3 on F123-CASTx129 with Sox2 tags
File
4DNFIG21QWDB
alignments (bam)
12.52 GB
-
File
4DNFI4G5CISG
contact list-replicate (pairs)
1.22 GB
-

Quality Metrics

Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Details
From Multiple Experiments
4DNES2NY639B
Multiple Experiments
File
Contact List-combined (pairs)
4DNFIQVG8HXI
122.78m
56.118%
30.838%
13.045%
Experiment
4DNEX9IAX7HP
Bio Rep 1, Tec Rep 1
PLAC-seq against H3K4me3 on F123-CASTx129 with Sox2 tags
File
Contact List-replicate (pairs)
4DNFICXRNO3Z
55.51m
55.596%
31.873%
12.531%
Experiment
4DNEXX456QN1
Bio Rep 2, Tec Rep 1
PLAC-seq against H3K4me3 on F123-CASTx129 with Sox2 tags
File
Contact List-replicate (pairs)
4DNFI4G5CISG
67.27m
56.548%
29.984%
13.468%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNES2NY639B
Multiple Experiments
File
Contact Matrix (mcool)
4DNFIEJ4ED21
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
4DNEX9IAX7HP
Bio Rep 1, Tec Rep 1
PLAC-seq against H3K4me3 on F123-CASTx129 with Sox2 tags
File
Alignments (bam)
4DNFITUJU2KV
135.76m
15.35%
15.986%
27.699%
0.076%
0.071%
Experiment
4DNEXX456QN1
Bio Rep 2, Tec Rep 1
PLAC-seq against H3K4me3 on F123-CASTx129 with Sox2 tags
File
Alignments (bam)
4DNFIG21QWDB
134.16m
14.124%
15.641%
20.027%
0.066%
0.09%