ExperimentSetReplicate

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ExperimentSet4DNESBU3XFPO
released
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Replicates of H3K4me3 PLAC-seq on Sox2 tagged F123 ES cells wih 2 CTCF binding sites introduced between Sox2 and its Super Enhancer

   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 between Sox2 and its 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
4DNESBU3XFPO
Multiple Experiments
File
4DNFI5DKDVI3
contact list-combined (pairs)
2.28 GB
-
File
4DNFI2FROTH3
contact matrix (hic)
999.38 MB
-
File
4DNFIHB3DJEX
contact matrix (mcool)
619.12 MB
Experiment
4DNEXZ7NM1MY
Bio Rep 1, Tec Rep 1
PLAC-seq against H3K4me3 on F123-CASTx129 with Sox2 tags and RMCE site between Sox2 and its SE
File
4DNFINBLQ4OL
alignments (bam)
13.41 GB
-
File
4DNFIS9NYX5X
contact list-replicate (pairs)
1.26 GB
-
Experiment
4DNEX4W1UDR5
Bio Rep 2, Tec Rep 1
PLAC-seq against H3K4me3 on F123-CASTx129 with Sox2 tags and RMCE site between Sox2 and its SE
File
4DNFINCZV2KE
alignments (bam)
13.18 GB
-
File
4DNFI8EMNE97
contact list-replicate (pairs)
1.19 GB
-

Quality Metrics

Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Details
From Multiple Experiments
4DNESBU3XFPO
Multiple Experiments
File
Contact List-combined (pairs)
4DNFI5DKDVI3
134.11m
57.139%
31.574%
11.287%
Experiment
4DNEXZ7NM1MY
Bio Rep 1, Tec Rep 1
PLAC-seq against H3K4me3 on F123-CASTx129 with Sox2 tags and RMCE site between Sox2 and its SE
File
Contact List-replicate (pairs)
4DNFIS9NYX5X
68.72m
58.556%
30.131%
11.312%
Experiment
4DNEX4W1UDR5
Bio Rep 2, Tec Rep 1
PLAC-seq against H3K4me3 on F123-CASTx129 with Sox2 tags and RMCE site between Sox2 and its SE
File
Contact List-replicate (pairs)
4DNFI8EMNE97
65.39m
55.65%
33.09%
11.26%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNESBU3XFPO
Multiple Experiments
File
Contact Matrix (mcool)
4DNFIHB3DJEX
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
4DNEXZ7NM1MY
Bio Rep 1, Tec Rep 1
PLAC-seq against H3K4me3 on F123-CASTx129 with Sox2 tags and RMCE site between Sox2 and its SE
File
Alignments (bam)
4DNFINBLQ4OL
141.75m
14.367%
18.617%
18.456%
0.08%
0.077%
Experiment
4DNEX4W1UDR5
Bio Rep 2, Tec Rep 1
PLAC-seq against H3K4me3 on F123-CASTx129 with Sox2 tags and RMCE site between Sox2 and its SE
File
Alignments (bam)
4DNFINCZV2KE
143.51m
15.034%
17.671%
21.643%
0.083%
0.075%