ExperimentSetReplicate

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ExperimentSet4DNESQTFP2CM
released
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Replicates of H3K4me3 PLAC-seq on Sox2 tagged F123 ES cells wih 4 CTCF binding sites introduced downstream of both Sox2 and its Super Enhancer - Control

   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 and RMCE site downstream of Sox2 SE
Experiment Type(s) 
PLAC-seq
Modification Type 
RMCE
Treatment Type 
None
Assay Details 
Target: H3K4me3

7 Processed Files

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Experiment
File
File Type
File Size
Notes
From Multiple Experiments
4DNESQTFP2CM
Multiple Experiments
File
4DNFIXIZNNC5
contact list-combined (pairs)
2.01 GB
-
File
4DNFI3SY22BY
contact matrix (hic)
865.76 MB
-
File
4DNFICAGE35X
contact matrix (mcool)
531.65 MB
Experiment
4DNEXME357DI
Bio Rep 1, Tec Rep 1
PLAC-seq against H3K4me3 on F123-CASTx129 with Sox2 tags and RMCE site downstream of Sox2 SE
File
4DNFI343W2LX
alignments (bam)
9.89 GB
-
File
4DNFIH1VFOLS
contact list-replicate (pairs)
882.49 MB
-
Experiment
4DNEXAEZWMHO
Bio Rep 2, Tec Rep 1
PLAC-seq against H3K4me3 on F123-CASTx129 with Sox2 tags and RMCE site downstream of Sox2 SE
File
4DNFIWTLLTKR
alignments (bam)
14.09 GB
-
File
4DNFIEN8SY1L
contact list-replicate (pairs)
1.31 GB
-

Quality Metrics

Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Details
From Multiple Experiments
4DNESQTFP2CM
Multiple Experiments
File
Contact List-combined (pairs)
4DNFIXIZNNC5
119.49m
56.794%
31.909%
11.297%
Experiment
4DNEXME357DI
Bio Rep 1, Tec Rep 1
PLAC-seq against H3K4me3 on F123-CASTx129 with Sox2 tags and RMCE site downstream of Sox2 SE
File
Contact List-replicate (pairs)
4DNFIH1VFOLS
47.43m
56.407%
33.448%
10.144%
Experiment
4DNEXAEZWMHO
Bio Rep 2, Tec Rep 1
PLAC-seq against H3K4me3 on F123-CASTx129 with Sox2 tags and RMCE site downstream of Sox2 SE
File
Contact List-replicate (pairs)
4DNFIEN8SY1L
72.06m
57.048%
30.896%
12.056%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNESQTFP2CM
Multiple Experiments
File
Contact Matrix (mcool)
4DNFICAGE35X
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
4DNEXME357DI
Bio Rep 1, Tec Rep 1
PLAC-seq against H3K4me3 on F123-CASTx129 with Sox2 tags and RMCE site downstream of Sox2 SE
File
Alignments (bam)
4DNFI343W2LX
110.84m
14.845%
16.66%
25.631%
0.075%
0.073%
Experiment
4DNEXAEZWMHO
Bio Rep 2, Tec Rep 1
PLAC-seq against H3K4me3 on F123-CASTx129 with Sox2 tags and RMCE site downstream of Sox2 SE
File
Alignments (bam)
4DNFIWTLLTKR
152.42m
13.996%
16.743%
21.915%
0.07%
0.076%