ExperimentSetReplicate

ExperimentSet4DNESTHV5FQK
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Replicates of H3K4me3 PLAC-seq on Sox2 tagged F123 ES cells wih 2 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

Quality Metrics

Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Report
Details
From Multiple Experiments
4DNESTHV5FQK
Multiple Experiments
File
Contact List-combined (pairs)
4DNFIAH9TM6S
130.6m
56.014%
32.148%
11.838%
Experiment
4DNEXPYK7QFL
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)
4DNFIV8ZZU3B
65.86m
57.213%
30.853%
11.933%
Experiment
4DNEXHX2T8OE
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)
4DNFIL1PUTGR
64.74m
54.794%
33.465%
11.741%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNESTHV5FQK
Multiple Experiments
File
Contact Matrix (mcool)
4DNFI6ONRQWY
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
4DNEXPYK7QFL
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)
4DNFIJ1EBFQO
134.23m
15.044%
18.412%
17.399%
0.078%
0.085%
Experiment
4DNEXHX2T8OE
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)
4DNFIWA17DGK
140.75m
15.152%
17.548%
21.219%
0.083%
0.084%